Starting phenix.real_space_refine
on Sat May 10 16:03:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wtd_37832/05_2025/8wtd_37832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wtd_37832/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wtd_37832/05_2025/8wtd_37832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wtd_37832/05_2025/8wtd_37832.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wtd_37832/05_2025/8wtd_37832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wtd_37832/05_2025/8wtd_37832.cif"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.64, per 1000 atoms: 0.72
  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: 1.69
  Conformation dependent library (CDL) restraints added in 966.4 milliseconds
  

  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: 0.81
  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: 1.83

  Time building geometry restraints manager: 1.98 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:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.280
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.660
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (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
 TRP   0.015   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A  34 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.027   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 457 

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

*********************** 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  : 0.744 
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: 0.1945
  time to fit residues: 30.2527
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  : 0.748 
-------------------------------------------------------------------------------
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 65 optimal weight:    0.5980
   chunk 59 optimal weight:    0.2980
   chunk 32 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.182754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.148699 restraints weight = 6712.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.86
r_work: 0.3459 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1468

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= 0.134
  Angle     :  0.573   7.419   9050  Z= 0.286
  Chirality :  0.043   0.171    955
  Planarity :  0.004   0.042   1165
  Dihedral  :  7.689  57.564    948
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 21.90 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.31), residues: 786
  helix:  1.00 (0.27), residues: 408
  sheet:  1.01 (0.79), residues: 44
  loop : -1.11 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.018   0.001   PHE A 369 
 TYR   0.010   0.001   TYR A 237 
 ARG   0.002   0.000   ARG B 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00238 (    4)
  link_NAG-ASN         : angle       1.80557 (   12)
  hydrogen bonds       : bond        0.03830 (  298)
  hydrogen bonds       : angle       4.43595 (  843)
  SS BOND              : bond        0.00632 (    6)
  SS BOND              : angle       1.59871 (   12)
  covalent geometry    : bond        0.00311 ( 6640)
  covalent geometry    : angle       0.56665 ( 9026)

*********************** 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
  105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7159 (tt0) cc_final: 0.6704 (mt-10)
REVERT: A  166 GLU cc_start: 0.7045 (tp30) cc_final: 0.6841 (tp30)
REVERT: A  168 TRP cc_start: 0.7495 (t-100) cc_final: 0.7240 (t-100)
REVERT: A  224 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6198 (mm-30)
REVERT: A  227 GLU cc_start: 0.7122 (tt0) cc_final: 0.6664 (mt-10)
REVERT: A  325 GLN cc_start: 0.7642 (tm130) cc_final: 0.7211 (tp-100)
REVERT: A  364 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7943 (t)
REVERT: A  402 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7257 (mt-10)
REVERT: A  423 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8336 (mt)
REVERT: A  480 MET cc_start: 0.8003 (mtp) cc_final: 0.7788 (mtp)
REVERT: A  547 SER cc_start: 0.8437 (t) cc_final: 0.8230 (t)
REVERT: A  552 GLN cc_start: 0.7809 (tp40) cc_final: 0.7580 (tp-100)
REVERT: A  562 LYS cc_start: 0.8481 (ttpp) cc_final: 0.7832 (tttt)
REVERT: A  577 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7811 (mtpp)
REVERT: A  589 GLU cc_start: 0.7481 (tp30) cc_final: 0.7227 (tp30)
  outliers start: 17
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1582
  time to fit residues: 22.4325
Evaluate side-chains
  91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   97 LEU
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  364 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  423 LEU
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 42 optimal weight:    0.7980
   chunk 68 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0470
   chunk 0 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.4678

-------------------------------------------------------------------------------
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 = 0.4033 r_free = 0.4033 target = 0.181566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.144769 restraints weight = 6742.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.01
r_work: 0.3481 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6650  Z= 0.113
  Angle     :  0.532   6.895   9050  Z= 0.264
  Chirality :  0.041   0.152    955
  Planarity :  0.004   0.040   1165
  Dihedral  :  6.022  51.837    945
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.83 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.05 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.30), residues: 786
  helix:  1.24 (0.27), residues: 400
  sheet:  0.79 (0.77), residues: 44
  loop : -1.08 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.006   0.001   HIS A  34 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A 237 
 ARG   0.001   0.000   ARG B 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    4)
  link_NAG-ASN         : angle       2.05121 (   12)
  hydrogen bonds       : bond        0.03541 (  298)
  hydrogen bonds       : angle       4.27482 (  843)
  SS BOND              : bond        0.00351 (    6)
  SS BOND              : angle       1.29827 (   12)
  covalent geometry    : bond        0.00258 ( 6640)
  covalent geometry    : angle       0.52561 ( 9026)

*********************** 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
  97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7656 (mmpt) cc_final: 0.7044 (mptt)
REVERT: A   75 GLU cc_start: 0.7325 (tt0) cc_final: 0.6737 (mt-10)
REVERT: A  102 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7309 (mt0)
REVERT: A  168 TRP cc_start: 0.7553 (t-100) cc_final: 0.7217 (t-100)
REVERT: A  224 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6209 (mm-30)
REVERT: A  227 GLU cc_start: 0.7270 (tt0) cc_final: 0.6709 (mt-10)
REVERT: A  325 GLN cc_start: 0.7760 (tm130) cc_final: 0.7281 (tp-100)
REVERT: A  364 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7904 (t)
REVERT: A  402 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7316 (mt-10)
REVERT: A  547 SER cc_start: 0.8529 (t) cc_final: 0.8316 (t)
REVERT: A  552 GLN cc_start: 0.7946 (tp40) cc_final: 0.7599 (tp40)
REVERT: A  562 LYS cc_start: 0.8628 (ttpp) cc_final: 0.7910 (tttt)
REVERT: A  577 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7738 (mtpp)
REVERT: A  589 GLU cc_start: 0.7611 (tp30) cc_final: 0.7308 (tp30)
  outliers start: 19
  outliers final: 12
  residues processed: 92
  average time/residue: 0.1460
  time to fit residues: 19.3075
Evaluate side-chains
  91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  281 LEU
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  364 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  441 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 71 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.178222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.143971 restraints weight = 6829.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.87
r_work: 0.3354 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6650  Z= 0.148
  Angle     :  0.560   7.448   9050  Z= 0.279
  Chirality :  0.042   0.135    955
  Planarity :  0.004   0.042   1165
  Dihedral  :  4.984  50.308    942
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.34 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 22.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.30), residues: 786
  helix:  1.13 (0.27), residues: 406
  sheet:  0.68 (0.75), residues: 44
  loop : -1.08 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A  34 
 PHE   0.020   0.001   PHE A 369 
 TYR   0.011   0.001   TYR A 237 
 ARG   0.001   0.000   ARG B 498 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00186 (    4)
  link_NAG-ASN         : angle       2.34328 (   12)
  hydrogen bonds       : bond        0.03957 (  298)
  hydrogen bonds       : angle       4.32434 (  843)
  SS BOND              : bond        0.00514 (    6)
  SS BOND              : angle       1.38017 (   12)
  covalent geometry    : bond        0.00354 ( 6640)
  covalent geometry    : angle       0.55163 ( 9026)

*********************** 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
  99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.783 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7706 (mmpt) cc_final: 0.7113 (mptt)
REVERT: A   75 GLU cc_start: 0.7285 (tt0) cc_final: 0.6741 (mt-10)
REVERT: A  168 TRP cc_start: 0.7857 (t-100) cc_final: 0.7472 (t-100)
REVERT: A  215 TYR cc_start: 0.8074 (m-80) cc_final: 0.7531 (m-80)
REVERT: A  224 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6263 (mm-30)
REVERT: A  227 GLU cc_start: 0.7189 (tt0) cc_final: 0.6725 (mt-10)
REVERT: A  323 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.5801 (ptp)
REVERT: A  325 GLN cc_start: 0.7943 (tm130) cc_final: 0.7463 (tp-100)
REVERT: A  402 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7340 (mt-10)
REVERT: A  547 SER cc_start: 0.8551 (t) cc_final: 0.8330 (t)
REVERT: A  562 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8037 (tttt)
REVERT: A  577 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7795 (mtmt)
REVERT: A  589 GLU cc_start: 0.7643 (tp30) cc_final: 0.7386 (tp30)
  outliers start: 13
  outliers final: 9
  residues processed: 93
  average time/residue: 0.1617
  time to fit residues: 21.4401
Evaluate side-chains
  91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  281 LEU
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 B residue  382 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 38 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0060
   chunk 55 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0970
   chunk 45 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.180207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.146638 restraints weight = 6742.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 1.93
r_work: 0.3396 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6650  Z= 0.115
  Angle     :  0.515   6.802   9050  Z= 0.258
  Chirality :  0.041   0.134    955
  Planarity :  0.004   0.042   1165
  Dihedral  :  4.767  53.165    942
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.71 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 23.20 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.30), residues: 786
  helix:  1.18 (0.27), residues: 405
  sheet:  0.68 (0.74), residues: 44
  loop : -1.06 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A  34 
 PHE   0.015   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A 237 
 ARG   0.001   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00170 (    4)
  link_NAG-ASN         : angle       2.04925 (   12)
  hydrogen bonds       : bond        0.03591 (  298)
  hydrogen bonds       : angle       4.25360 (  843)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       1.26703 (   12)
  covalent geometry    : bond        0.00266 ( 6640)
  covalent geometry    : angle       0.50812 ( 9026)

*********************** 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
  99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7528 (t70)
REVERT: A   68 LYS cc_start: 0.7754 (mmpt) cc_final: 0.7210 (mptt)
REVERT: A   75 GLU cc_start: 0.7298 (tt0) cc_final: 0.6791 (mt-10)
REVERT: A  102 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7580 (mm-40)
REVERT: A  168 TRP cc_start: 0.7914 (t-100) cc_final: 0.7565 (t-100)
REVERT: A  224 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6287 (mm-30)
REVERT: A  227 GLU cc_start: 0.7186 (tt0) cc_final: 0.6727 (mt-10)
REVERT: A  323 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.5586 (ptp)
REVERT: A  325 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7499 (tp-100)
REVERT: A  353 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8683 (mtpt)
REVERT: A  547 SER cc_start: 0.8529 (t) cc_final: 0.8318 (t)
REVERT: A  562 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8035 (tttt)
REVERT: A  577 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7694 (mtmt)
  outliers start: 16
  outliers final: 10
  residues processed: 94
  average time/residue: 0.1616
  time to fit residues: 21.4084
Evaluate side-chains
  90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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  281 LEU
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  353 LYS
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    0.1980
   chunk 48 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.179199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.144241 restraints weight = 6766.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 1.84
r_work: 0.3401 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2608

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= 0.125
  Angle     :  0.524   6.917   9050  Z= 0.264
  Chirality :  0.041   0.132    955
  Planarity :  0.004   0.041   1165
  Dihedral  :  4.712  54.580    942
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.09 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.20 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.30), residues: 786
  helix:  1.27 (0.27), residues: 398
  sheet:  0.62 (0.74), residues: 44
  loop : -1.10 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.010   0.001   TYR A 237 
 ARG   0.001   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00152 (    4)
  link_NAG-ASN         : angle       1.96531 (   12)
  hydrogen bonds       : bond        0.03703 (  298)
  hydrogen bonds       : angle       4.27017 (  843)
  SS BOND              : bond        0.00419 (    6)
  SS BOND              : angle       1.40720 (   12)
  covalent geometry    : bond        0.00293 ( 6640)
  covalent geometry    : angle       0.51751 ( 9026)

*********************** 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
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7529 (t70)
REVERT: A   60 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6839 (mm-40)
REVERT: A   68 LYS cc_start: 0.7629 (mmpt) cc_final: 0.7035 (mptt)
REVERT: A   75 GLU cc_start: 0.7213 (tt0) cc_final: 0.6652 (mt-10)
REVERT: A  168 TRP cc_start: 0.7980 (t-100) cc_final: 0.7658 (t-100)
REVERT: A  215 TYR cc_start: 0.8028 (m-80) cc_final: 0.7526 (m-80)
REVERT: A  224 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6193 (mm-30)
REVERT: A  227 GLU cc_start: 0.7060 (tt0) cc_final: 0.6714 (mt-10)
REVERT: A  323 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.6017 (mtt)
REVERT: A  325 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7414 (tp-100)
REVERT: A  353 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8685 (mtpt)
REVERT: A  364 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7897 (t)
REVERT: A  402 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7226 (mt-10)
REVERT: A  467 GLU cc_start: 0.4364 (OUTLIER) cc_final: 0.4063 (pm20)
REVERT: A  547 SER cc_start: 0.8531 (t) cc_final: 0.8281 (t)
REVERT: A  562 LYS cc_start: 0.8645 (ttpp) cc_final: 0.7956 (tttt)
REVERT: A  577 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7697 (mtmt)
REVERT: B  493 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.6625 (tm-30)
  outliers start: 20
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1510
  time to fit residues: 21.0355
Evaluate side-chains
  104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
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  281 LEU
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  353 LYS
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  382 VAL
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 9 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    0.2980
   chunk 56 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0970
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.182393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.146137 restraints weight = 6755.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.27
r_work: 0.3489 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6650  Z= 0.110
  Angle     :  0.502   6.555   9050  Z= 0.254
  Chirality :  0.041   0.131    955
  Planarity :  0.004   0.041   1165
  Dihedral  :  4.581  56.281    942
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.45 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.78 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.30), residues: 786
  helix:  1.34 (0.27), residues: 397
  sheet:  0.69 (0.73), residues: 44
  loop : -1.09 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00163 (    4)
  link_NAG-ASN         : angle       1.82677 (   12)
  hydrogen bonds       : bond        0.03469 (  298)
  hydrogen bonds       : angle       4.21850 (  843)
  SS BOND              : bond        0.00338 (    6)
  SS BOND              : angle       1.21927 (   12)
  covalent geometry    : bond        0.00252 ( 6640)
  covalent geometry    : angle       0.49643 ( 9026)

*********************** 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
  102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7735 (mmpt) cc_final: 0.7120 (mptt)
REVERT: A   75 GLU cc_start: 0.7296 (tt0) cc_final: 0.6700 (mt-10)
REVERT: A  102 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7497 (mm-40)
REVERT: A  168 TRP cc_start: 0.8063 (t-100) cc_final: 0.7796 (t-100)
REVERT: A  215 TYR cc_start: 0.8113 (m-80) cc_final: 0.7586 (m-80)
REVERT: A  224 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6292 (mm-30)
REVERT: A  227 GLU cc_start: 0.7178 (tt0) cc_final: 0.6810 (mt-10)
REVERT: A  325 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7624 (tm-30)
REVERT: A  353 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8772 (mtpt)
REVERT: A  364 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7878 (t)
REVERT: A  476 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6431 (tptp)
REVERT: A  547 SER cc_start: 0.8573 (t) cc_final: 0.8328 (t)
REVERT: A  562 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8033 (tttt)
REVERT: A  577 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7691 (mtmt)
REVERT: B  493 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.6835 (tm-30)
  outliers start: 17
  outliers final: 9
  residues processed: 97
  average time/residue: 0.1581
  time to fit residues: 21.6002
Evaluate side-chains
  95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 20 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.176034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.140946 restraints weight = 6869.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.22
r_work: 0.3408 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6650  Z= 0.183
  Angle     :  0.590   7.543   9050  Z= 0.295
  Chirality :  0.044   0.156    955
  Planarity :  0.004   0.040   1165
  Dihedral  :  4.467  27.546    940
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.63 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.30), residues: 786
  helix:  0.99 (0.26), residues: 408
  sheet:  0.67 (0.73), residues: 44
  loop : -1.14 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.019   0.002   PHE A 369 
 TYR   0.013   0.002   TYR A 385 
 ARG   0.003   0.001   ARG B 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    4)
  link_NAG-ASN         : angle       2.06280 (   12)
  hydrogen bonds       : bond        0.04244 (  298)
  hydrogen bonds       : angle       4.43839 (  843)
  SS BOND              : bond        0.00564 (    6)
  SS BOND              : angle       1.57559 (   12)
  covalent geometry    : bond        0.00445 ( 6640)
  covalent geometry    : angle       0.58270 ( 9026)

*********************** 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
  100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6952 (mm-40)
REVERT: A   68 LYS cc_start: 0.7827 (mmpt) cc_final: 0.7208 (mptt)
REVERT: A  215 TYR cc_start: 0.8264 (m-80) cc_final: 0.7804 (m-80)
REVERT: A  224 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6331 (mm-30)
REVERT: A  227 GLU cc_start: 0.7266 (tt0) cc_final: 0.6883 (mt-10)
REVERT: A  325 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7586 (tm-30)
REVERT: A  353 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8822 (mtpt)
REVERT: A  467 GLU cc_start: 0.4793 (OUTLIER) cc_final: 0.4440 (pm20)
REVERT: A  476 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6477 (tptp)
REVERT: A  547 SER cc_start: 0.8597 (t) cc_final: 0.8348 (t)
REVERT: A  562 LYS cc_start: 0.8823 (ttpp) cc_final: 0.8138 (tttt)
REVERT: A  577 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7774 (mtmt)
  outliers start: 17
  outliers final: 11
  residues processed: 95
  average time/residue: 0.1567
  time to fit residues: 21.0064
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  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  420 SER
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  428 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0970
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7578

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.178258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.141993 restraints weight = 6931.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.14
r_work: 0.3440 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2934

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= 0.137
  Angle     :  0.541   6.842   9050  Z= 0.272
  Chirality :  0.042   0.130    955
  Planarity :  0.004   0.044   1165
  Dihedral  :  4.284  27.012    940
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.71 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 23.78 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.30), residues: 786
  helix:  1.10 (0.26), residues: 403
  sheet:  0.68 (0.72), residues: 44
  loop : -1.12 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.010   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00164 (    4)
  link_NAG-ASN         : angle       1.95383 (   12)
  hydrogen bonds       : bond        0.03837 (  298)
  hydrogen bonds       : angle       4.36528 (  843)
  SS BOND              : bond        0.00405 (    6)
  SS BOND              : angle       1.44162 (   12)
  covalent geometry    : bond        0.00326 ( 6640)
  covalent geometry    : angle       0.53408 ( 9026)

*********************** 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
  98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.757 
Fit side-chains
REVERT: A   60 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6954 (mm-40)
REVERT: A   68 LYS cc_start: 0.7750 (mmpt) cc_final: 0.7123 (mptt)
REVERT: A  215 TYR cc_start: 0.8153 (m-80) cc_final: 0.7637 (m-80)
REVERT: A  224 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6257 (mm-30)
REVERT: A  227 GLU cc_start: 0.7229 (tt0) cc_final: 0.6845 (mt-10)
REVERT: A  325 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7503 (tm-30)
REVERT: A  353 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8788 (mtpt)
REVERT: A  364 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7933 (t)
REVERT: A  467 GLU cc_start: 0.4846 (OUTLIER) cc_final: 0.3469 (pm20)
REVERT: A  476 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6469 (tptp)
REVERT: A  494 ASP cc_start: 0.7731 (m-30) cc_final: 0.7432 (t70)
REVERT: A  547 SER cc_start: 0.8586 (t) cc_final: 0.8325 (t)
REVERT: A  562 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8048 (tttt)
REVERT: A  577 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7714 (mtmt)
REVERT: A  582 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6918 (mmm160)
REVERT: B  365 TYR cc_start: 0.8201 (m-80) cc_final: 0.7999 (m-80)
REVERT: B  493 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.6853 (tm-30)
  outliers start: 15
  outliers final: 9
  residues processed: 95
  average time/residue: 0.1725
  time to fit residues: 22.6800
Evaluate side-chains
  97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
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  467 GLU
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  582 ARG
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.173471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.139052 restraints weight = 6959.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.91
r_work: 0.3413 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6650  Z= 0.189
  Angle     :  0.602   7.579   9050  Z= 0.301
  Chirality :  0.044   0.162    955
  Planarity :  0.004   0.043   1165
  Dihedral  :  4.594  28.802    940
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.34 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.34 %
    Favored  : 74.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.30), residues: 786
  helix:  0.89 (0.26), residues: 409
  sheet:  0.74 (0.73), residues: 44
  loop : -1.14 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.018   0.002   PHE A 369 
 TYR   0.012   0.002   TYR A 385 
 ARG   0.003   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00234 (    4)
  link_NAG-ASN         : angle       2.09248 (   12)
  hydrogen bonds       : bond        0.04356 (  298)
  hydrogen bonds       : angle       4.51470 (  843)
  SS BOND              : bond        0.00523 (    6)
  SS BOND              : angle       1.68246 (   12)
  covalent geometry    : bond        0.00461 ( 6640)
  covalent geometry    : angle       0.59453 ( 9026)

********************** 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
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7884 (mmpt) cc_final: 0.7271 (mptt)
REVERT: A  215 TYR cc_start: 0.8279 (m-80) cc_final: 0.7811 (m-80)
REVERT: A  224 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6382 (mm-30)
REVERT: A  227 GLU cc_start: 0.7302 (tt0) cc_final: 0.6931 (mt-10)
REVERT: A  341 LYS cc_start: 0.7550 (tttt) cc_final: 0.7319 (ttmt)
REVERT: A  353 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8817 (mtpt)
REVERT: A  364 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.8018 (t)
REVERT: A  462 MET cc_start: 0.8458 (mtp) cc_final: 0.8249 (mtp)
REVERT: A  467 GLU cc_start: 0.4869 (OUTLIER) cc_final: 0.3524 (pm20)
REVERT: A  476 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6546 (tptp)
REVERT: A  494 ASP cc_start: 0.7769 (m-30) cc_final: 0.7474 (t0)
REVERT: A  547 SER cc_start: 0.8609 (t) cc_final: 0.8366 (t)
REVERT: A  562 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8166 (tttt)
REVERT: A  577 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7803 (mtmt)
REVERT: A  582 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6969 (mmm160)
REVERT: B  493 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.6940 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 100
  average time/residue: 0.1840
  time to fit residues: 25.1840
Evaluate side-chains
  102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
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  467 GLU
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  582 ARG
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0000
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4584

-------------------------------------------------------------------------------
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 = 0.4011 r_free = 0.4011 target = 0.179723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.143256 restraints weight = 6989.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.30
r_work: 0.3460 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6650  Z= 0.113
  Angle     :  0.523   6.645   9050  Z= 0.264
  Chirality :  0.041   0.130    955
  Planarity :  0.004   0.044   1165
  Dihedral  :  4.193  26.648    940
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.58 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 24.35 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.30), residues: 786
  helix:  1.10 (0.26), residues: 403
  sheet:  0.75 (0.74), residues: 44
  loop : -1.06 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A 237 
 ARG   0.002   0.000   ARG A 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00192 (    4)
  link_NAG-ASN         : angle       1.85434 (   12)
  hydrogen bonds       : bond        0.03634 (  298)
  hydrogen bonds       : angle       4.35724 (  843)
  SS BOND              : bond        0.00343 (    6)
  SS BOND              : angle       1.32444 (   12)
  covalent geometry    : bond        0.00259 ( 6640)
  covalent geometry    : angle       0.51727 ( 9026)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3817.52 seconds
wall clock time: 66 minutes 46.95 seconds (4006.95 seconds total)