Starting phenix.real_space_refine
on Fri Aug 22 17:41:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wtd_37832/08_2025/8wtd_37832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wtd_37832/08_2025/8wtd_37832.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wtd_37832/08_2025/8wtd_37832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wtd_37832/08_2025/8wtd_37832.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wtd_37832/08_2025/8wtd_37832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wtd_37832/08_2025/8wtd_37832.map"
  }
  resolution = 3.06
  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=   0.072
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    4134      2.51       5
     N    1069      2.21       5
     O    1216      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6456
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 4845
          Classifications: {'peptide': 594}
          Link IDs: {'PTRANS': 27, 'TRANS': 566}
    Chain: "B"
      Number of atoms: 1555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1555
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 14, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.84, per 1000 atoms: 0.29
  Number of scatterers: 6456
  At special positions: 0
  Unit cell: (73.528, 91.304, 117.16, 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    1216      8.00
     N    1069      7.00
     C    4134      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, 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 B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=1.99

  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 901 " - " ASN A 546 "
      " NAG A 902 " - " ASN A  90 "
      " NAG A 903 " - " ASN A 322 "
      " NAG A 904 " - " ASN A  53 "
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 370.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 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:
      34 helices and 5 sheets defined
      53.8% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 29
    Processing helix  chain 'A' and resid 31 through 53
      removed outlier: 3.935A  pdb=" N   GLU A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 79
      removed outlier: 3.545A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
    Processing helix  chain 'A' and resid 91 through 101
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 154
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.721A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.991A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    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
      removed outlier: 3.630A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    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 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 4.156A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.578A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.679A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 446
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.745A  pdb=" N   GLU A 483 " --> pdb=" O   GLU A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.115A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.543A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   CYS A 542 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 538 through 542'
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.852A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.738A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.692A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 3.533A  pdb=" N   PHE B 371 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 389
      removed outlier: 3.601A  pdb=" N   ASP B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 386 through 389'
    Processing helix  chain 'B' and resid 406 through 410
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.233A  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 350
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.531A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ASN B 437 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   PHE B 374 " --> pdb=" O   ASN B 437 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.356A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 454
      removed outlier: 8.324A  pdb=" N   ASN B 450 " --> pdb=" O   SER B 494 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   SER B 494 " --> pdb=" O   ASN B 450 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   LEU B 452 " --> pdb=" O   LEU B 492 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   LEU B 492 " --> pdb=" O   LEU B 452 " (cutoff:3.500A)

    298 hydrogen bonds defined for protein.
    843 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1069
        1.29 -     1.42: 1837
        1.42 -     1.55: 3676
        1.55 -     1.68: 0
        1.68 -     1.81: 58
  Bond restraints: 6640
  Sorted by residual:
  bond pdb=" C   PRO B 491 "
       pdb=" O   PRO B 491 "
    ideal  model  delta    sigma   weight residual
    1.235  1.156  0.079 1.30e-02 5.92e+03 3.70e+01
  bond pdb=" CA  ALA A  36 "
       pdb=" CB  ALA A  36 "
    ideal  model  delta    sigma   weight residual
    1.529  1.450  0.079 1.58e-02 4.01e+03 2.50e+01
  bond pdb=" CA  SER B 494 "
       pdb=" CB  SER B 494 "
    ideal  model  delta    sigma   weight residual
    1.532  1.454  0.077 1.59e-02 3.96e+03 2.38e+01
  bond pdb=" CA  SER B 490 "
       pdb=" CB  SER B 490 "
    ideal  model  delta    sigma   weight residual
    1.526  1.454  0.073 1.53e-02 4.27e+03 2.25e+01
  bond pdb=" C   PRO B 486 "
       pdb=" O   PRO B 486 "
    ideal  model  delta    sigma   weight residual
    1.233  1.190  0.043 9.60e-03 1.09e+04 2.03e+01
  ... (remaining 6635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 8794
        2.52 -     5.03: 176
        5.03 -     7.55: 36
        7.55 -    10.07: 14
       10.07 -    12.58: 6
  Bond angle restraints: 9026
  Sorted by residual:
  angle pdb=" N   LYS A  31 "
        pdb=" CA  LYS A  31 "
        pdb=" C   LYS A  31 "
      ideal   model   delta    sigma   weight residual
     113.72  102.68   11.04 1.30e+00 5.92e-01 7.21e+01
  angle pdb=" C   PRO B 486 "
        pdb=" CA  PRO B 486 "
        pdb=" CB  PRO B 486 "
      ideal   model   delta    sigma   weight residual
     111.40  103.78    7.62 9.10e-01 1.21e+00 7.02e+01
  angle pdb=" CA  ASP A  30 "
        pdb=" CB  ASP A  30 "
        pdb=" CG  ASP A  30 "
      ideal   model   delta    sigma   weight residual
     112.60  120.71   -8.11 1.00e+00 1.00e+00 6.58e+01
  angle pdb=" N   PRO B 491 "
        pdb=" CA  PRO B 491 "
        pdb=" CB  PRO B 491 "
      ideal   model   delta    sigma   weight residual
     103.25   95.40    7.85 1.05e+00 9.07e-01 5.58e+01
  angle pdb=" N   TYR B 489 "
        pdb=" CA  TYR B 489 "
        pdb=" CB  TYR B 489 "
      ideal   model   delta    sigma   weight residual
     110.49  123.07  -12.58 1.69e+00 3.50e-01 5.54e+01
  ... (remaining 9021 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.48: 3455
       20.48 -    40.96: 393
       40.96 -    61.43: 110
       61.43 -    81.91: 10
       81.91 -   102.39: 10
  Dihedral angle restraints: 3978
    sinusoidal: 1658
      harmonic: 2320
  Sorted by residual:
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.78   54.22     1      1.00e+01 1.00e-02 3.99e+01
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.16  -54.16     1      1.00e+01 1.00e-02 3.98e+01
  dihedral pdb=" C   PHE A  28 "
           pdb=" N   PHE A  28 "
           pdb=" CA  PHE A  28 "
           pdb=" CB  PHE A  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.45  -14.15     0      2.50e+00 1.60e-01 3.20e+01
  ... (remaining 3975 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 822
       0.068 -    0.135: 111
       0.135 -    0.203: 12
       0.203 -    0.271: 8
       0.271 -    0.338: 2
  Chirality restraints: 955
  Sorted by residual:
  chirality pdb=" CA  PHE A  28 "
            pdb=" N   PHE A  28 "
            pdb=" C   PHE A  28 "
            pdb=" CB  PHE A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.86e+00
  chirality pdb=" CA  CYS B 488 "
            pdb=" N   CYS B 488 "
            pdb=" C   CYS B 488 "
            pdb=" CB  CYS B 488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" CA  ASN B 487 "
            pdb=" N   ASN B 487 "
            pdb=" C   ASN B 487 "
            pdb=" CB  ASN B 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.80e+00
  ... (remaining 952 not shown)

  Planarity restraints: 1169
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  81 "   -0.025 2.00e-02 2.50e+03   5.01e-02 2.51e+01
        pdb=" C   GLN A  81 "    0.087 2.00e-02 2.50e+03
        pdb=" O   GLN A  81 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   MET A  82 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 470 "   -0.017 2.00e-02 2.50e+03   3.14e-02 9.84e+00
        pdb=" C   THR B 470 "    0.054 2.00e-02 2.50e+03
        pdb=" O   THR B 470 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU B 471 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 478 "   -0.043 5.00e-02 4.00e+02   6.54e-02 6.83e+00
        pdb=" N   PRO B 479 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 479 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 479 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1166 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1201
        2.77 -     3.30: 6090
        3.30 -     3.83: 11023
        3.83 -     4.37: 12761
        4.37 -     4.90: 22451
  Nonbonded interactions: 53526
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD1 ASP A 509 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OG  SER B 438 "
            pdb=" OD2 ASP B 442 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OH  TYR A 215 "
            pdb=" OE1 GLU A 571 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" O   VAL A 485 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   ASP A 499 "
            pdb=" OG  SER A 502 "
     model   vdw
     2.268 3.040
  ... (remaining 53521 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:             2.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.060
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079   6650  Z= 0.348
  Angle     :  0.912  12.584   9050  Z= 0.566
  Chirality :  0.053   0.338    955
  Planarity :  0.004   0.065   1165
  Dihedral  : 18.482 102.391   2470
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  5.34 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 23.34 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.94 %
  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 aren not related in a simple way.
  whole: -0.02 (0.31), residues: 786
  helix:  0.90 (0.27), residues: 403
  sheet:  1.39 (0.86), residues: 44
  loop : -1.35 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.027   0.001   TYR B 453 
 PHE   0.017   0.001   PHE A 369 
 TRP   0.015   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 6640)
  covalent geometry    : angle       0.90108 ( 9026)
  SS BOND              : bond        0.01612 (    6)
  SS BOND              : angle       3.76098 (   12)
  hydrogen bonds       : bond        0.12672 (  298)
  hydrogen bonds       : angle       5.49318 (  843)
  link_NAG-ASN         : bond        0.00118 (    4)
  link_NAG-ASN         : angle       1.62922 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.6860 (tt0) cc_final: 0.6326 (mt-10)
REVERT: A  102 GLN cc_start: 0.7864 (mm110) cc_final: 0.7586 (mm-40)
REVERT: A  168 TRP cc_start: 0.7271 (t-100) cc_final: 0.6659 (t-100)
REVERT: A  224 GLU cc_start: 0.5770 (mt-10) cc_final: 0.5432 (mm-30)
REVERT: A  227 GLU cc_start: 0.6494 (tt0) cc_final: 0.5957 (mt-10)
REVERT: A  325 GLN cc_start: 0.7254 (tm130) cc_final: 0.7025 (tp-100)
REVERT: A  402 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7198 (mt-10)
REVERT: A  480 MET cc_start: 0.7646 (mtp) cc_final: 0.7376 (mtp)
REVERT: A  547 SER cc_start: 0.8332 (t) cc_final: 0.7914 (p)
REVERT: A  552 GLN cc_start: 0.7398 (tp40) cc_final: 0.7114 (tp40)
REVERT: A  562 LYS cc_start: 0.8300 (ttpp) cc_final: 0.7512 (mttp)
REVERT: A  577 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7628 (mtpp)
REVERT: A  589 GLU cc_start: 0.6757 (tp30) cc_final: 0.6483 (tp30)
REVERT: B  356 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8294 (tttm)
REVERT: B  471 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7121 (mt-10)
REVERT: B  493 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7035 (tm130)
  outliers start: 5
  outliers final: 1
  residues processed: 118
  average time/residue: 0.0813
  time to fit residues: 12.8426
Evaluate side-chains
  93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  493 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.0970
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0570
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 531 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.182918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.148911 restraints weight = 6780.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.80
r_work: 0.3478 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6650  Z= 0.119
  Angle     :  0.555   7.293   9050  Z= 0.278
  Chirality :  0.042   0.172    955
  Planarity :  0.004   0.043   1165
  Dihedral  :  7.775  57.280    948
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.33 %
    Favored  : 75.50 %
  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 aren not related in a simple way.
  whole:  0.25 (0.31), residues: 786
  helix:  1.13 (0.27), residues: 399
  sheet:  1.04 (0.79), residues: 44
  loop : -1.11 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 559 
 TYR   0.008   0.001   TYR A 237 
 PHE   0.015   0.001   PHE A 369 
 TRP   0.009   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6640)
  covalent geometry    : angle       0.54875 ( 9026)
  SS BOND              : bond        0.00686 (    6)
  SS BOND              : angle       1.59877 (   12)
  hydrogen bonds       : bond        0.03651 (  298)
  hydrogen bonds       : angle       4.40630 (  843)
  link_NAG-ASN         : bond        0.00220 (    4)
  link_NAG-ASN         : angle       1.74048 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7180 (tt0) cc_final: 0.6704 (mt-10)
REVERT: A  166 GLU cc_start: 0.7006 (tp30) cc_final: 0.6782 (tp30)
REVERT: A  168 TRP cc_start: 0.7349 (t-100) cc_final: 0.7085 (t-100)
REVERT: A  224 GLU cc_start: 0.6493 (mt-10) cc_final: 0.6153 (mm-30)
REVERT: A  227 GLU cc_start: 0.7159 (tt0) cc_final: 0.6651 (mt-10)
REVERT: A  325 GLN cc_start: 0.7563 (tm130) cc_final: 0.7156 (tp-100)
REVERT: A  364 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7936 (t)
REVERT: A  402 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7247 (mt-10)
REVERT: A  552 GLN cc_start: 0.7757 (tp40) cc_final: 0.7471 (tp-100)
REVERT: A  562 LYS cc_start: 0.8395 (ttpp) cc_final: 0.7756 (tttt)
REVERT: A  577 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7774 (mtpp)
REVERT: A  589 GLU cc_start: 0.7468 (tp30) cc_final: 0.7219 (tp30)
  outliers start: 15
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0577
  time to fit residues: 7.9859
Evaluate side-chains
  84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
B 493 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.179172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.144228 restraints weight = 6692.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.81
r_work: 0.3412 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6650  Z= 0.142
  Angle     :  0.575   7.575   9050  Z= 0.285
  Chirality :  0.043   0.142    955
  Planarity :  0.004   0.040   1165
  Dihedral  :  5.895  51.381    945
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.19 %
    Favored  : 74.93 %
  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 aren not related in a simple way.
  whole:  0.26 (0.30), residues: 786
  helix:  1.14 (0.27), residues: 406
  sheet:  0.75 (0.76), residues: 44
  loop : -1.10 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 355 
 TYR   0.012   0.001   TYR A 237 
 PHE   0.022   0.002   PHE A 369 
 TRP   0.010   0.001   TRP A 168 
 HIS   0.007   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6640)
  covalent geometry    : angle       0.56761 ( 9026)
  SS BOND              : bond        0.00569 (    6)
  SS BOND              : angle       1.45863 (   12)
  hydrogen bonds       : bond        0.03989 (  298)
  hydrogen bonds       : angle       4.36096 (  843)
  link_NAG-ASN         : bond        0.00283 (    4)
  link_NAG-ASN         : angle       2.24277 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7593 (mmpt) cc_final: 0.7013 (mptt)
REVERT: A   75 GLU cc_start: 0.7238 (tt0) cc_final: 0.6720 (mt-10)
REVERT: A  168 TRP cc_start: 0.7742 (t-100) cc_final: 0.7494 (t-100)
REVERT: A  224 GLU cc_start: 0.6449 (mt-10) cc_final: 0.6159 (mm-30)
REVERT: A  227 GLU cc_start: 0.7097 (tt0) cc_final: 0.6646 (mt-10)
REVERT: A  323 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.6147 (mtt)
REVERT: A  325 GLN cc_start: 0.7808 (tm130) cc_final: 0.7337 (tp-100)
REVERT: A  402 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7256 (mt-10)
REVERT: A  562 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8001 (tttt)
REVERT: A  577 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7777 (mtpp)
REVERT: A  589 GLU cc_start: 0.7545 (tp30) cc_final: 0.7286 (tp30)
REVERT: B  498 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8233 (mtt180)
  outliers start: 20
  outliers final: 10
  residues processed: 96
  average time/residue: 0.0561
  time to fit residues: 7.7378
Evaluate side-chains
  90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  498 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
A 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.173498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.138805 restraints weight = 6837.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 1.89
r_work: 0.3318 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6650  Z= 0.202
  Angle     :  0.623   8.051   9050  Z= 0.311
  Chirality :  0.045   0.142    955
  Planarity :  0.005   0.043   1165
  Dihedral  :  5.285  47.152    942
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.85 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.20 %
    Favored  : 74.35 %
  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 aren not related in a simple way.
  whole: -0.05 (0.30), residues: 786
  helix:  0.73 (0.26), residues: 417
  sheet:  0.70 (0.75), residues: 44
  loop : -1.11 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 245 
 TYR   0.013   0.002   TYR A 237 
 PHE   0.022   0.002   PHE A 369 
 TRP   0.010   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 6640)
  covalent geometry    : angle       0.61419 ( 9026)
  SS BOND              : bond        0.00733 (    6)
  SS BOND              : angle       1.66279 (   12)
  hydrogen bonds       : bond        0.04498 (  298)
  hydrogen bonds       : angle       4.50585 (  843)
  link_NAG-ASN         : bond        0.00280 (    4)
  link_NAG-ASN         : angle       2.53104 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6847 (mm-40)
REVERT: A   68 LYS cc_start: 0.7823 (mmpt) cc_final: 0.7238 (mptt)
REVERT: A  102 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7694 (mm-40)
REVERT: A  168 TRP cc_start: 0.7903 (t-100) cc_final: 0.7510 (t-100)
REVERT: A  215 TYR cc_start: 0.8173 (m-80) cc_final: 0.7691 (m-80)
REVERT: A  224 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6352 (mm-30)
REVERT: A  227 GLU cc_start: 0.7281 (tt0) cc_final: 0.6814 (mt-10)
REVERT: A  323 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6215 (ptp)
REVERT: A  325 GLN cc_start: 0.7985 (tm130) cc_final: 0.7502 (tp-100)
REVERT: A  402 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7311 (mt-10)
REVERT: A  467 GLU cc_start: 0.4542 (OUTLIER) cc_final: 0.4082 (pm20)
REVERT: A  577 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7806 (mtmt)
  outliers start: 17
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0578
  time to fit residues: 7.8916
Evaluate side-chains
  92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  428 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    0.0370
   chunk 27 optimal weight:    0.7980
   chunk 71 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0050
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.2072

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.182267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.147441 restraints weight = 6814.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.83
r_work: 0.3433 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6650  Z= 0.097
  Angle     :  0.503   6.404   9050  Z= 0.253
  Chirality :  0.040   0.136    955
  Planarity :  0.004   0.041   1165
  Dihedral  :  4.750  52.587    942
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.20 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.77 %
    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 aren not related in a simple way.
  whole:  0.30 (0.30), residues: 786
  helix:  1.29 (0.27), residues: 391
  sheet:  0.64 (0.75), residues: 44
  loop : -1.13 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.007   0.001   TYR A 237 
 PHE   0.012   0.001   PHE A 369 
 TRP   0.007   0.001   TRP A 168 
 HIS   0.005   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 6640)
  covalent geometry    : angle       0.49312 ( 9026)
  SS BOND              : bond        0.00247 (    6)
  SS BOND              : angle       1.16113 (   12)
  hydrogen bonds       : bond        0.03394 (  298)
  hydrogen bonds       : angle       4.25011 (  843)
  link_NAG-ASN         : bond        0.00233 (    4)
  link_NAG-ASN         : angle       2.56567 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6793 (mm-40)
REVERT: A   68 LYS cc_start: 0.7642 (mmpt) cc_final: 0.7048 (mptt)
REVERT: A   75 GLU cc_start: 0.7135 (tt0) cc_final: 0.6579 (mt-10)
REVERT: A  168 TRP cc_start: 0.7924 (t-100) cc_final: 0.7665 (t-100)
REVERT: A  224 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6207 (mm-30)
REVERT: A  227 GLU cc_start: 0.7051 (tt0) cc_final: 0.6673 (mt-10)
REVERT: A  325 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7463 (tp-100)
REVERT: A  353 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8715 (mtpt)
REVERT: A  364 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7817 (t)
REVERT: A  476 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6279 (tptp)
REVERT: A  577 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7655 (mtmt)
  outliers start: 15
  outliers final: 8
  residues processed: 91
  average time/residue: 0.0651
  time to fit residues: 8.4876
Evaluate side-chains
  87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  428 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 45 optimal weight:    0.1980
   chunk 58 optimal weight:    0.0030
   chunk 29 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.181441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.146140 restraints weight = 6908.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.02
r_work: 0.3457 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6650  Z= 0.119
  Angle     :  0.525   6.891   9050  Z= 0.265
  Chirality :  0.041   0.131    955
  Planarity :  0.004   0.041   1165
  Dihedral  :  4.210  26.429    940
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.33 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 22.91 %
    Favored  : 74.93 %
  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 aren not related in a simple way.
  whole:  0.36 (0.30), residues: 786
  helix:  1.30 (0.27), residues: 398
  sheet:  0.67 (0.74), residues: 44
  loop : -1.10 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 219 
 TYR   0.015   0.001   TYR B 365 
 PHE   0.016   0.001   PHE A 369 
 TRP   0.008   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6640)
  covalent geometry    : angle       0.51810 ( 9026)
  SS BOND              : bond        0.00367 (    6)
  SS BOND              : angle       1.31351 (   12)
  hydrogen bonds       : bond        0.03610 (  298)
  hydrogen bonds       : angle       4.25100 (  843)
  link_NAG-ASN         : bond        0.00167 (    4)
  link_NAG-ASN         : angle       2.12637 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.8052 (tp30) cc_final: 0.6889 (mt-10)
REVERT: A   60 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6835 (mm-40)
REVERT: A   68 LYS cc_start: 0.7631 (mmpt) cc_final: 0.7061 (mptt)
REVERT: A   75 GLU cc_start: 0.7134 (tt0) cc_final: 0.6563 (mt-10)
REVERT: A  168 TRP cc_start: 0.8112 (t-100) cc_final: 0.7864 (t-100)
REVERT: A  215 TYR cc_start: 0.8003 (m-80) cc_final: 0.7546 (m-80)
REVERT: A  224 GLU cc_start: 0.6541 (mt-10) cc_final: 0.6221 (mm-30)
REVERT: A  227 GLU cc_start: 0.7000 (tt0) cc_final: 0.6669 (mt-10)
REVERT: A  325 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7471 (tp-100)
REVERT: A  353 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8720 (mtpt)
REVERT: A  476 LYS cc_start: 0.6592 (OUTLIER) cc_final: 0.6324 (tptp)
REVERT: A  577 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7678 (mtmt)
REVERT: B  493 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6657 (tm-30)
  outliers start: 15
  outliers final: 9
  residues processed: 89
  average time/residue: 0.0584
  time to fit residues: 7.3903
Evaluate side-chains
  88 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0670
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.182357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.146704 restraints weight = 6803.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.23
r_work: 0.3481 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6650  Z= 0.108
  Angle     :  0.504   6.951   9050  Z= 0.255
  Chirality :  0.041   0.130    955
  Planarity :  0.004   0.041   1165
  Dihedral  :  4.048  25.635    940
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.45 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 22.91 %
    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 aren not related in a simple way.
  whole:  0.41 (0.30), residues: 786
  helix:  1.35 (0.27), residues: 397
  sheet:  0.73 (0.74), residues: 44
  loop : -1.09 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 177 
 TYR   0.008   0.001   TYR A 237 
 PHE   0.014   0.001   PHE A 369 
 TRP   0.009   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6640)
  covalent geometry    : angle       0.49720 ( 9026)
  SS BOND              : bond        0.00349 (    6)
  SS BOND              : angle       1.24105 (   12)
  hydrogen bonds       : bond        0.03415 (  298)
  hydrogen bonds       : angle       4.19974 (  843)
  link_NAG-ASN         : bond        0.00156 (    4)
  link_NAG-ASN         : angle       1.95169 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6956 (mm-40)
REVERT: A   68 LYS cc_start: 0.7780 (mmpt) cc_final: 0.7176 (mptt)
REVERT: A   75 GLU cc_start: 0.7301 (tt0) cc_final: 0.6682 (mt-10)
REVERT: A  215 TYR cc_start: 0.8090 (m-80) cc_final: 0.7623 (m-80)
REVERT: A  224 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6295 (mm-30)
REVERT: A  227 GLU cc_start: 0.7177 (tt0) cc_final: 0.6797 (mt-10)
REVERT: A  325 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7565 (tp-100)
REVERT: A  353 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8784 (mtpt)
REVERT: A  364 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7912 (t)
REVERT: A  408 MET cc_start: 0.7953 (mpp) cc_final: 0.7590 (mmm)
REVERT: A  494 ASP cc_start: 0.7724 (m-30) cc_final: 0.7423 (t70)
REVERT: A  562 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8043 (tttt)
REVERT: A  577 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7658 (mtmt)
REVERT: B  493 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.6795 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 92
  average time/residue: 0.0638
  time to fit residues: 8.2978
Evaluate side-chains
  86 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.1980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.179046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.142403 restraints weight = 6916.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.30
r_work: 0.3452 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6650  Z= 0.136
  Angle     :  0.539   7.612   9050  Z= 0.272
  Chirality :  0.042   0.132    955
  Planarity :  0.004   0.041   1165
  Dihedral  :  4.171  26.634    940
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.45 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 22.48 %
    Favored  : 75.50 %
  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 aren not related in a simple way.
  whole:  0.34 (0.30), residues: 786
  helix:  1.20 (0.26), residues: 406
  sheet:  0.79 (0.74), residues: 44
  loop : -1.06 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.014   0.001   TYR B 365 
 PHE   0.017   0.001   PHE A 369 
 TRP   0.010   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6640)
  covalent geometry    : angle       0.53252 ( 9026)
  SS BOND              : bond        0.00402 (    6)
  SS BOND              : angle       1.34746 (   12)
  hydrogen bonds       : bond        0.03798 (  298)
  hydrogen bonds       : angle       4.27802 (  843)
  link_NAG-ASN         : bond        0.00195 (    4)
  link_NAG-ASN         : angle       1.98088 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.8202 (tp30) cc_final: 0.6879 (mt-10)
REVERT: A   68 LYS cc_start: 0.7750 (mmpt) cc_final: 0.7124 (mptt)
REVERT: A  215 TYR cc_start: 0.8146 (m-80) cc_final: 0.7717 (m-80)
REVERT: A  224 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6258 (mm-30)
REVERT: A  227 GLU cc_start: 0.7199 (tt0) cc_final: 0.6800 (mt-10)
REVERT: A  325 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7599 (tp-100)
REVERT: A  353 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8801 (mtpt)
REVERT: A  364 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7962 (t)
REVERT: A  476 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6435 (tptp)
REVERT: A  494 ASP cc_start: 0.7736 (m-30) cc_final: 0.7445 (t0)
REVERT: A  577 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7657 (mtmt)
REVERT: B  493 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6809 (tm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 93
  average time/residue: 0.0659
  time to fit residues: 8.8246
Evaluate side-chains
  92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.178827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.142412 restraints weight = 6930.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.27
r_work: 0.3455 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6650  Z= 0.134
  Angle     :  0.534   7.366   9050  Z= 0.270
  Chirality :  0.042   0.131    955
  Planarity :  0.004   0.042   1165
  Dihedral  :  4.154  26.473    940
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.33 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 22.77 %
    Favored  : 75.22 %
  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 aren not related in a simple way.
  whole:  0.29 (0.30), residues: 786
  helix:  1.13 (0.26), residues: 406
  sheet:  0.79 (0.74), residues: 44
  loop : -1.06 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.009   0.001   TYR A 237 
 PHE   0.016   0.001   PHE A 369 
 TRP   0.010   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6640)
  covalent geometry    : angle       0.52715 ( 9026)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       1.39584 (   12)
  hydrogen bonds       : bond        0.03756 (  298)
  hydrogen bonds       : angle       4.31218 (  843)
  link_NAG-ASN         : bond        0.00239 (    4)
  link_NAG-ASN         : angle       1.97303 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.7758 (mmpt) cc_final: 0.7125 (mptt)
REVERT: A  215 TYR cc_start: 0.8129 (m-80) cc_final: 0.7643 (m-80)
REVERT: A  224 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6284 (mm-30)
REVERT: A  227 GLU cc_start: 0.7206 (tt0) cc_final: 0.6838 (mt-10)
REVERT: A  325 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7606 (tp-100)
REVERT: A  353 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8797 (mtpt)
REVERT: A  364 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7918 (t)
REVERT: A  476 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6447 (tptp)
REVERT: A  494 ASP cc_start: 0.7710 (m-30) cc_final: 0.7431 (t0)
REVERT: A  577 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7660 (mtmt)
REVERT: B  493 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.6794 (tm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 91
  average time/residue: 0.0633
  time to fit residues: 8.3776
Evaluate side-chains
  91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0570
   chunk 50 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.180676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.144173 restraints weight = 6843.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.28
r_work: 0.3472 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6650  Z= 0.118
  Angle     :  0.523   7.304   9050  Z= 0.264
  Chirality :  0.041   0.130    955
  Planarity :  0.004   0.041   1165
  Dihedral  :  4.039  25.935    940
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.33 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 23.20 %
    Favored  : 74.64 %
  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 aren not related in a simple way.
  whole:  0.32 (0.30), residues: 786
  helix:  1.16 (0.26), residues: 402
  sheet:  0.78 (0.74), residues: 44
  loop : -1.02 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.009   0.001   TYR A 237 
 PHE   0.015   0.001   PHE A 369 
 TRP   0.009   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6640)
  covalent geometry    : angle       0.51673 ( 9026)
  SS BOND              : bond        0.00361 (    6)
  SS BOND              : angle       1.28022 (   12)
  hydrogen bonds       : bond        0.03602 (  298)
  hydrogen bonds       : angle       4.30203 (  843)
  link_NAG-ASN         : bond        0.00184 (    4)
  link_NAG-ASN         : angle       1.86730 (   12)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.7768 (mmpt) cc_final: 0.7135 (mptt)
REVERT: A  215 TYR cc_start: 0.8120 (m-80) cc_final: 0.7644 (m-80)
REVERT: A  224 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6256 (mm-30)
REVERT: A  227 GLU cc_start: 0.7146 (tt0) cc_final: 0.6788 (mt-10)
REVERT: A  353 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8793 (mtpt)
REVERT: A  364 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7913 (t)
REVERT: A  408 MET cc_start: 0.7950 (mpp) cc_final: 0.7550 (mmm)
REVERT: A  476 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6456 (tptp)
REVERT: A  494 ASP cc_start: 0.7644 (m-30) cc_final: 0.7394 (t0)
REVERT: A  577 LYS cc_start: 0.7867 (mtmt) cc_final: 0.7587 (mtmt)
REVERT: B  493 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.6811 (tm-30)
  outliers start: 15
  outliers final: 11
  residues processed: 89
  average time/residue: 0.0670
  time to fit residues: 8.4574
Evaluate side-chains
  90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0970
   chunk 67 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 59 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 64 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.180258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.143469 restraints weight = 6878.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.30
r_work: 0.3467 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6650  Z= 0.123
  Angle     :  0.527   7.332   9050  Z= 0.266
  Chirality :  0.042   0.130    955
  Planarity :  0.004   0.041   1165
  Dihedral  :  4.018  25.576    940
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.45 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.20 %
    Favored  : 74.35 %
  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 aren not related in a simple way.
  whole:  0.33 (0.30), residues: 786
  helix:  1.16 (0.26), residues: 402
  sheet:  0.75 (0.74), residues: 44
  loop : -0.98 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.015   0.001   TYR B 365 
 PHE   0.015   0.001   PHE A 369 
 TRP   0.009   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6640)
  covalent geometry    : angle       0.52183 ( 9026)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       1.30824 (   12)
  hydrogen bonds       : bond        0.03651 (  298)
  hydrogen bonds       : angle       4.30689 (  843)
  link_NAG-ASN         : bond        0.00175 (    4)
  link_NAG-ASN         : angle       1.81612 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1728.18 seconds
wall clock time: 30 minutes 17.14 seconds (1817.14 seconds total)