Starting phenix.real_space_refine
on Tue Aug  4 19:45:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ysr_73426/08_2026/9ysr_73426.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ysr_73426/08_2026/9ysr_73426.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ysr_73426/08_2026/9ysr_73426.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ysr_73426/08_2026/9ysr_73426.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ysr_73426/08_2026/9ysr_73426.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ysr_73426/08_2026/9ysr_73426.map"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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      32      5.16       5
     C    4024      2.51       5
     N    1035      2.21       5
     O    1182      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6273
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4673
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 571, 4665
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 25, 'TRANS': 545}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 571, 4665
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 25, 'TRANS': 545}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 4786
    Chain: "B"
      Number of atoms: 1516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1516
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 11, 'TRANS': 174}
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 1.93, per 1000 atoms: 0.31
  Number of scatterers: 6273
  At special positions: 0
  Unit cell: (74.048, 90.688, 112.32, 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      32     16.00
     O    1182      8.00
     N    1035      7.00
     C    4024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    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 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A  53 "
      " NAG A 702 " - " ASN A 322 "
      " NAG A 703 " - " ASN A 546 "
      " NAG A 704 " - " ASN A  90 "
      " NAG A 705 " - " ASN A 103 "
      " NAG A 706 " - " ASN A 432 "
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 299.9 milliseconds
  

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 4 sheets defined
      56.5% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
    Processing helix  chain 'A' and resid 55 through 83
      removed outlier: 3.700A  pdb=" N   TYR A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
    Processing helix  chain 'A' and resid 104 through 108
      removed outlier: 3.700A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 125
      removed outlier: 3.732A  pdb=" N   SER A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 155
      removed outlier: 4.075A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.769A  pdb=" N   TRP A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.866A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.605A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.526A  pdb=" N   TYR A 279 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 300
      removed outlier: 3.578A  pdb=" N   VAL A 298 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLN A 300 " --> pdb=" O   ALA A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.520A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.942A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 397 through 414
      removed outlier: 4.048A  pdb=" N   HIS A 401 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLU A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.646A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 3.983A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 503 through 508
      removed outlier: 3.513A  pdb=" N   ASN A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.130A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.980A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.529A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 366 through 370
    Processing helix  chain 'B' and resid 386 through 390
      removed outlier: 3.604A  pdb=" N   LEU B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 407
      No H-bonds generated for 'chain 'B' and resid 405 through 407'
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.975A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352
      removed outlier: 5.322A  pdb=" N   ALA A 348 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU A 359 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   ASP A 350 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   ARG A 357 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY A 352 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.543A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454

    299 hydrogen bonds defined for protein.
    863 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.64

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1982
        1.34 -     1.46: 1356
        1.46 -     1.58: 3062
        1.58 -     1.70: 0
        1.70 -     1.81: 53
  Bond restraints: 6453
  Sorted by residual:
  bond pdb=" N   VAL A 574 "
       pdb=" CA  VAL A 574 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.28e-02 6.10e+03 8.76e+00
  bond pdb=" N   ILE A 379 "
       pdb=" CA  ILE A 379 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.30e-02 5.92e+03 8.11e+00
  bond pdb=" N   VAL A 506 "
       pdb=" CA  VAL A 506 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.30e-02 5.92e+03 7.62e+00
  bond pdb=" N   THR B 470 "
       pdb=" CA  THR B 470 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.16e-02 7.43e+03 7.47e+00
  bond pdb=" N   GLN B 493 "
       pdb=" CA  GLN B 493 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.21e-02 6.83e+03 6.82e+00
  ... (remaining 6448 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 8639
        2.37 -     4.75: 115
        4.75 -     7.12: 9
        7.12 -     9.50: 1
        9.50 -    11.87: 1
  Bond angle restraints: 8765
  Sorted by residual:
  angle pdb=" CB  MET A 270 "
        pdb=" CG  MET A 270 "
        pdb=" SD  MET A 270 "
      ideal   model   delta    sigma   weight residual
     112.70  124.57  -11.87 3.00e+00 1.11e-01 1.57e+01
  angle pdb=" CA  LEU A 266 "
        pdb=" C   LEU A 266 "
        pdb=" O   LEU A 266 "
      ideal   model   delta    sigma   weight residual
     122.44  118.07    4.37 1.34e+00 5.57e-01 1.06e+01
  angle pdb=" C   PRO B 491 "
        pdb=" N   LEU B 492 "
        pdb=" CA  LEU B 492 "
      ideal   model   delta    sigma   weight residual
     122.77  118.95    3.82 1.33e+00 5.65e-01 8.26e+00
  angle pdb=" CA  SER B 494 "
        pdb=" C   SER B 494 "
        pdb=" O   SER B 494 "
      ideal   model   delta    sigma   weight residual
     121.55  118.53    3.02 1.06e+00 8.90e-01 8.12e+00
  angle pdb=" N   LEU A  45 "
        pdb=" CA  LEU A  45 "
        pdb=" C   LEU A  45 "
      ideal   model   delta    sigma   weight residual
     111.36  108.35    3.01 1.09e+00 8.42e-01 7.63e+00
  ... (remaining 8760 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3351
       17.95 -    35.90: 370
       35.90 -    53.85: 126
       53.85 -    71.79: 16
       71.79 -    89.74: 8
  Dihedral angle restraints: 3871
    sinusoidal: 1642
      harmonic: 2229
  Sorted by residual:
  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
     -86.00 -169.75   83.75     1      1.00e+01 1.00e-02 8.55e+01
  dihedral pdb=" CA  CYS B 480 "
           pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   14.79   64.21     1      2.00e+01 2.50e-03 1.36e+01
  dihedral pdb=" CB  GLU A 312 "
           pdb=" CG  GLU A 312 "
           pdb=" CD  GLU A 312 "
           pdb=" OE1 GLU A 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.74  -89.74     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 3868 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 670
       0.042 -    0.085: 183
       0.085 -    0.127: 64
       0.127 -    0.169: 7
       0.169 -    0.212: 3
  Chirality restraints: 927
  Sorted by residual:
  chirality pdb=" CG  LEU B 455 "
            pdb=" CB  LEU B 455 "
            pdb=" CD1 LEU B 455 "
            pdb=" CD2 LEU B 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" C1  NAG A 705 "
            pdb=" ND2 ASN A 103 "
            pdb=" C2  NAG A 705 "
            pdb=" O5  NAG A 705 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ILE B 358 "
            pdb=" N   ILE B 358 "
            pdb=" C   ILE B 358 "
            pdb=" CB  ILE B 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.01e-01
  ... (remaining 924 not shown)

  Planarity restraints: 1129
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 273 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.44e+00
        pdb=" C   ARG A 273 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ARG A 273 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE A 274 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 372 "   -0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO B 373 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 373 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 373 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  41 "    0.010 2.00e-02 2.50e+03   8.92e-03 1.59e+00
        pdb=" CG  TYR A  41 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  41 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  41 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  41 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  41 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  41 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A  41 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1126 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 3204
        2.99 -     3.47: 6541
        3.47 -     3.94: 10542
        3.94 -     4.42: 12251
        4.42 -     4.90: 18851
  Nonbonded interactions: 51389
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 415 "
            pdb=" OD2 ASP B 420 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" OG1 THR B 376 "
            pdb=" OG  SER B 435 "
     model   vdw
     2.555 3.040
  nonbonded pdb=" N   ASN B 478 "
            pdb=" OD1 ASN B 478 "
     model   vdw
     2.573 3.120
  nonbonded pdb=" C   SER B 359 "
            pdb=" OG  SER B 359 "
     model   vdw
     2.616 2.616
  nonbonded pdb=" N   ASP A 206 "
            pdb=" OD1 ASP A 206 "
     model   vdw
     2.619 3.120
  ... (remaining 51384 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.42 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.230
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
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      :  0.003   0.039   6463  Z= 0.216
  Angle     :  0.659  11.875   8791  Z= 0.382
  Chirality :  0.045   0.212    927
  Planarity :  0.004   0.039   1123
  Dihedral  : 16.635  89.743   2427
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 24.25 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.30), residues: 750
  helix:  0.78 (0.26), residues: 378
  sheet: -0.58 (0.77), residues: 44
  loop : -0.75 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 466 
 TYR   0.022   0.001   TYR A  41 
 PHE   0.018   0.002   PHE A 230 
 TRP   0.015   0.001   TRP A 566 
 HIS   0.008   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.22 ( 6453)
  covalent geometry    : angle       0.65388 /  0.38 ( 8765)
  SS BOND              : bond        0.00484 /  0.24 (    4)
  SS BOND              : angle       0.86600 /  0.48 (    8)
  hydrogen bonds       : bond        0.12939 /  9.20 (  299)
  hydrogen bonds       : angle       5.78138 /  4.20 (  863)
  link_NAG-ASN         : bond        0.00444 /  0.23 (    6)
  link_NAG-ASN         : angle       1.84852 /  1.05 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 173
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASN cc_start: 0.7719 (m-40) cc_final: 0.7378 (m110)
REVERT: A   73 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8501 (mt)
REVERT: A  152 MET cc_start: 0.6473 (mmm) cc_final: 0.5634 (mmm)
REVERT: A  288 LYS cc_start: 0.8516 (mmpt) cc_final: 0.8257 (mmtm)
REVERT: A  313 LYS cc_start: 0.7406 (mttt) cc_final: 0.7044 (mtpp)
REVERT: A  375 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6669 (mm-30)
REVERT: A  455 MET cc_start: 0.6946 (tmm) cc_final: 0.6686 (tmm)
REVERT: A  472 GLN cc_start: 0.6836 (mt0) cc_final: 0.6581 (pt0)
REVERT: A  479 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6477 (tm-30)
REVERT: A  482 ARG cc_start: 0.7359 (mtt180) cc_final: 0.7153 (mtt-85)
REVERT: A  529 LEU cc_start: 0.8301 (mt) cc_final: 0.8080 (mm)
REVERT: A  552 GLN cc_start: 0.7977 (tp40) cc_final: 0.7739 (tp40)
REVERT: A  564 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6956 (mm-30)
REVERT: B  374 PHE cc_start: 0.6588 (m-80) cc_final: 0.6095 (m-10)
REVERT: B  394 ASN cc_start: 0.7502 (m-40) cc_final: 0.7092 (m-40)
REVERT: B  438 SER cc_start: 0.8484 (p) cc_final: 0.8082 (p)
REVERT: B  494 SER cc_start: 0.8428 (m) cc_final: 0.8144 (m)
REVERT: B  495 TYR cc_start: 0.7879 (m-80) cc_final: 0.7538 (t80)
REVERT: B  511 VAL cc_start: 0.8402 (t) cc_final: 0.8012 (m)
  outliers start: 4
  outliers final: 3
  residues processed: 175
  average time/residue: 0.0630
  time to fit residues: 14.7777
Evaluate side-chains
  172 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  542 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.3980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  24 GLN
** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 325 GLN
** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
A 505 HIS
B 487 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.123531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.107765 restraints weight = 12977.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.111490 restraints weight = 5551.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.113844 restraints weight = 2991.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.115378 restraints weight = 1899.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.116126 restraints weight = 1352.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6463  Z= 0.199
  Angle     :  0.584   8.576   8791  Z= 0.306
  Chirality :  0.044   0.234    927
  Planarity :  0.004   0.038   1123
  Dihedral  :  5.193  44.866    959
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.01 %
    Favored  : 74.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.17 (0.30), residues: 750
  helix:  0.82 (0.26), residues: 382
  sheet: -0.33 (0.76), residues: 43
  loop : -0.58 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.017   0.001   TYR A  41 
 PHE   0.027   0.002   PHE B 497 
 TRP   0.016   0.002   TRP A 203 
 HIS   0.010   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.20 ( 6453)
  covalent geometry    : angle       0.57726 /  0.30 ( 8765)
  SS BOND              : bond        0.00393 /  0.19 (    4)
  SS BOND              : angle       0.98815 /  0.53 (    8)
  hydrogen bonds       : bond        0.05273 /  3.73 (  299)
  hydrogen bonds       : angle       5.19617 /  3.83 (  863)
  link_NAG-ASN         : bond        0.00421 /  0.21 (    6)
  link_NAG-ASN         : angle       1.98696 /  1.19 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 201
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7222 (mt0) cc_final: 0.6973 (mt0)
REVERT: A   37 GLU cc_start: 0.7211 (tt0) cc_final: 0.6702 (tt0)
REVERT: A   61 ASN cc_start: 0.7674 (m-40) cc_final: 0.7367 (m110)
REVERT: A  152 MET cc_start: 0.6595 (mmm) cc_final: 0.5974 (mmm)
REVERT: A  221 GLN cc_start: 0.7218 (tt0) cc_final: 0.6922 (tt0)
REVERT: A  288 LYS cc_start: 0.8575 (mmpt) cc_final: 0.8341 (mmtp)
REVERT: A  297 MET cc_start: 0.7847 (tpp) cc_final: 0.7563 (tpp)
REVERT: A  313 LYS cc_start: 0.7456 (mttt) cc_final: 0.7059 (mtpp)
REVERT: A  375 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6691 (mm-30)
REVERT: A  376 MET cc_start: 0.7533 (mtp) cc_final: 0.7231 (ttp)
REVERT: A  393 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7679 (ttm170)
REVERT: A  455 MET cc_start: 0.6947 (tmm) cc_final: 0.6676 (tmm)
REVERT: A  474 MET cc_start: 0.4941 (mmt) cc_final: 0.4075 (mmt)
REVERT: A  479 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6362 (tm-30)
REVERT: A  552 GLN cc_start: 0.8016 (tp40) cc_final: 0.7765 (tp-100)
REVERT: A  559 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7176 (ptp90)
REVERT: A  564 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7038 (mm-30)
REVERT: A  571 GLU cc_start: 0.7789 (tp30) cc_final: 0.7541 (tp30)
REVERT: B  347 PHE cc_start: 0.8536 (m-80) cc_final: 0.8314 (m-80)
REVERT: B  401 VAL cc_start: 0.8581 (t) cc_final: 0.8313 (p)
REVERT: B  429 PHE cc_start: 0.8463 (t80) cc_final: 0.7984 (t80)
REVERT: B  438 SER cc_start: 0.8618 (p) cc_final: 0.8233 (p)
REVERT: B  494 SER cc_start: 0.8432 (m) cc_final: 0.8211 (m)
REVERT: B  511 VAL cc_start: 0.8409 (t) cc_final: 0.7954 (m)
REVERT: B  512 VAL cc_start: 0.8816 (t) cc_final: 0.8492 (p)
  outliers start: 21
  outliers final: 13
  residues processed: 208
  average time/residue: 0.0558
  time to fit residues: 15.8029
Evaluate side-chains
  210 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 196
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  302 TRP
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  542 CYS
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0770
   chunk 38 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0770
   chunk 71 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0980
   chunk 13 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    0.1980
   overall best weight:    0.2096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
A 599 ASN
B 417 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.125470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.107755 restraints weight = 19954.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.112320 restraints weight = 7441.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115174 restraints weight = 3710.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.117008 restraints weight = 2215.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.118237 restraints weight = 1510.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6463  Z= 0.128
  Angle     :  0.540   6.683   8791  Z= 0.279
  Chirality :  0.041   0.221    927
  Planarity :  0.004   0.043   1123
  Dihedral  :  4.743  39.384    954
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.80 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.31), residues: 750
  helix:  0.96 (0.26), residues: 381
  sheet:  0.01 (0.77), residues: 44
  loop : -0.52 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 482 
 TYR   0.015   0.001   TYR A 385 
 PHE   0.024   0.002   PHE B 497 
 TRP   0.012   0.001   TRP A 566 
 HIS   0.009   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.13 ( 6453)
  covalent geometry    : angle       0.53399 /  0.28 ( 8765)
  SS BOND              : bond        0.00315 /  0.15 (    4)
  SS BOND              : angle       1.05690 /  0.58 (    8)
  hydrogen bonds       : bond        0.04652 /  3.27 (  299)
  hydrogen bonds       : angle       4.98779 /  3.69 (  863)
  link_NAG-ASN         : bond        0.00410 /  0.21 (    6)
  link_NAG-ASN         : angle       1.69625 /  1.02 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 186
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7213 (mt0) cc_final: 0.6990 (mt0)
REVERT: A   35 GLU cc_start: 0.6901 (tt0) cc_final: 0.6587 (mt-10)
REVERT: A   61 ASN cc_start: 0.7665 (m-40) cc_final: 0.7360 (m110)
REVERT: A   87 GLU cc_start: 0.7430 (tp30) cc_final: 0.6954 (mp0)
REVERT: A  152 MET cc_start: 0.6506 (mmm) cc_final: 0.5948 (mmm)
REVERT: A  185 VAL cc_start: 0.8422 (m) cc_final: 0.8150 (p)
REVERT: A  221 GLN cc_start: 0.7076 (tt0) cc_final: 0.6841 (tt0)
REVERT: A  288 LYS cc_start: 0.8551 (mmpt) cc_final: 0.8313 (mmtm)
REVERT: A  297 MET cc_start: 0.7804 (tpp) cc_final: 0.7542 (tpp)
REVERT: A  313 LYS cc_start: 0.7392 (mttt) cc_final: 0.6971 (mtpp)
REVERT: A  350 ASP cc_start: 0.7471 (t0) cc_final: 0.7242 (t0)
REVERT: A  375 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6637 (mm-30)
REVERT: A  455 MET cc_start: 0.6948 (tmm) cc_final: 0.6697 (tmm)
REVERT: A  474 MET cc_start: 0.5018 (mmt) cc_final: 0.4112 (mmt)
REVERT: A  479 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6426 (tm-30)
REVERT: A  482 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6993 (mtt90)
REVERT: A  552 GLN cc_start: 0.7980 (tp40) cc_final: 0.7681 (tp-100)
REVERT: A  559 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7164 (ptp90)
REVERT: A  564 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7033 (mm-30)
REVERT: A  571 GLU cc_start: 0.7786 (tp30) cc_final: 0.7568 (tp30)
REVERT: A  595 LEU cc_start: 0.7949 (mp) cc_final: 0.7707 (mp)
REVERT: B  357 ARG cc_start: 0.8103 (ttp-110) cc_final: 0.7849 (ttp-110)
REVERT: B  511 VAL cc_start: 0.8434 (t) cc_final: 0.7996 (m)
REVERT: B  512 VAL cc_start: 0.8782 (t) cc_final: 0.8471 (p)
  outliers start: 20
  outliers final: 10
  residues processed: 197
  average time/residue: 0.0547
  time to fit residues: 14.4337
Evaluate side-chains
  192 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 181
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  302 TRP
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  474 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0370
   chunk 24 optimal weight:    0.1980
   chunk 70 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 71 optimal weight:    0.5980
   chunk 34 optimal weight:    0.2980
   chunk 74 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.2658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.108368 restraints weight = 15231.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.112390 restraints weight = 6246.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.114972 restraints weight = 3293.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.116585 restraints weight = 2045.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.117687 restraints weight = 1445.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3475
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3475 r_free = 0.3475    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3475
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6463  Z= 0.144
  Angle     :  0.577   7.562   8791  Z= 0.299
  Chirality :  0.042   0.228    927
  Planarity :  0.004   0.037   1123
  Dihedral  :  4.794  38.914    953
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 24.55 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.31), residues: 750
  helix:  0.96 (0.26), residues: 382
  sheet:  0.05 (0.78), residues: 44
  loop : -0.51 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 177 
 TYR   0.020   0.001   TYR A  41 
 PHE   0.022   0.001   PHE B 497 
 TRP   0.012   0.001   TRP B 452 
 HIS   0.010   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 6453)
  covalent geometry    : angle       0.56210 /  0.29 ( 8765)
  SS BOND              : bond        0.00424 /  0.21 (    4)
  SS BOND              : angle       3.60334 /  1.82 (    8)
  hydrogen bonds       : bond        0.04666 /  3.30 (  299)
  hydrogen bonds       : angle       4.91194 /  3.64 (  863)
  link_NAG-ASN         : bond        0.00377 /  0.19 (    6)
  link_NAG-ASN         : angle       1.79957 /  1.08 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 186
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7196 (mt0) cc_final: 0.6940 (mt0)
REVERT: A   35 GLU cc_start: 0.6914 (tt0) cc_final: 0.6583 (mt-10)
REVERT: A   37 GLU cc_start: 0.7218 (tt0) cc_final: 0.6814 (tt0)
REVERT: A   61 ASN cc_start: 0.7667 (m-40) cc_final: 0.7372 (m110)
REVERT: A   87 GLU cc_start: 0.7433 (tp30) cc_final: 0.6932 (mp0)
REVERT: A  152 MET cc_start: 0.6568 (mmm) cc_final: 0.5982 (mmm)
REVERT: A  185 VAL cc_start: 0.8446 (m) cc_final: 0.8180 (p)
REVERT: A  190 MET cc_start: 0.7437 (ttm) cc_final: 0.7160 (ttp)
REVERT: A  221 GLN cc_start: 0.7064 (tt0) cc_final: 0.6796 (tt0)
REVERT: A  288 LYS cc_start: 0.8570 (mmpt) cc_final: 0.8331 (mmtp)
REVERT: A  297 MET cc_start: 0.7822 (tpp) cc_final: 0.7547 (tpp)
REVERT: A  312 GLU cc_start: 0.6678 (tt0) cc_final: 0.6364 (tt0)
REVERT: A  313 LYS cc_start: 0.7483 (mttt) cc_final: 0.7073 (mtpp)
REVERT: A  350 ASP cc_start: 0.7499 (t0) cc_final: 0.7243 (t0)
REVERT: A  368 ASP cc_start: 0.6898 (t70) cc_final: 0.6590 (t70)
REVERT: A  375 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6620 (mm-30)
REVERT: A  440 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7780 (tt)
REVERT: A  455 MET cc_start: 0.6946 (tmm) cc_final: 0.6692 (tmm)
REVERT: A  474 MET cc_start: 0.5048 (mmt) cc_final: 0.4775 (mmt)
REVERT: A  479 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6410 (tm-30)
REVERT: A  488 VAL cc_start: 0.8350 (m) cc_final: 0.7916 (m)
REVERT: A  522 GLN cc_start: 0.7977 (pt0) cc_final: 0.7648 (pt0)
REVERT: A  552 GLN cc_start: 0.7934 (tp40) cc_final: 0.7672 (tp-100)
REVERT: A  559 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7177 (ptp90)
REVERT: A  564 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7072 (mm-30)
REVERT: A  571 GLU cc_start: 0.7761 (tp30) cc_final: 0.7523 (tp30)
REVERT: B  357 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7905 (ttp-110)
REVERT: B  458 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7962 (mmmt)
REVERT: B  511 VAL cc_start: 0.8452 (t) cc_final: 0.8014 (m)
  outliers start: 25
  outliers final: 16
  residues processed: 201
  average time/residue: 0.0540
  time to fit residues: 14.6781
Evaluate side-chains
  199 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  302 TRP
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  443 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 47 optimal weight:    0.0970
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0980
   chunk 33 optimal weight:    0.2980
   chunk 12 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   chunk 41 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0970
   chunk 56 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.1576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.125456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.106501 restraints weight = 25341.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.111489 restraints weight = 8681.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.114608 restraints weight = 4164.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.116570 restraints weight = 2417.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.117899 restraints weight = 1621.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3497
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6463  Z= 0.120
  Angle     :  0.560   7.265   8791  Z= 0.289
  Chirality :  0.041   0.222    927
  Planarity :  0.004   0.036   1123
  Dihedral  :  4.708  39.017    953
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 25.15 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.31), residues: 750
  helix:  1.12 (0.26), residues: 383
  sheet: -0.02 (0.78), residues: 44
  loop : -0.50 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 482 
 TYR   0.020   0.001   TYR A  41 
 PHE   0.016   0.001   PHE B 497 
 TRP   0.011   0.001   TRP A 566 
 HIS   0.009   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 ( 6453)
  covalent geometry    : angle       0.54800 /  0.28 ( 8765)
  SS BOND              : bond        0.00808 /  0.40 (    4)
  SS BOND              : angle       3.02021 /  1.54 (    8)
  hydrogen bonds       : bond        0.04439 /  3.12 (  299)
  hydrogen bonds       : angle       4.81690 /  3.59 (  863)
  link_NAG-ASN         : bond        0.00395 /  0.20 (    6)
  link_NAG-ASN         : angle       1.66939 /  1.01 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7177 (mt0) cc_final: 0.6886 (mt0)
REVERT: A   35 GLU cc_start: 0.6875 (tt0) cc_final: 0.6444 (mt-10)
REVERT: A   61 ASN cc_start: 0.7695 (m-40) cc_final: 0.7386 (m110)
REVERT: A   87 GLU cc_start: 0.7406 (tp30) cc_final: 0.6936 (mp0)
REVERT: A  152 MET cc_start: 0.6495 (mmm) cc_final: 0.5940 (mmm)
REVERT: A  185 VAL cc_start: 0.8437 (m) cc_final: 0.8181 (p)
REVERT: A  221 GLN cc_start: 0.6997 (tt0) cc_final: 0.6719 (tt0)
REVERT: A  288 LYS cc_start: 0.8551 (mmpt) cc_final: 0.8298 (mmtm)
REVERT: A  297 MET cc_start: 0.7817 (tpp) cc_final: 0.7575 (tpp)
REVERT: A  312 GLU cc_start: 0.6796 (tt0) cc_final: 0.6380 (tt0)
REVERT: A  313 LYS cc_start: 0.7438 (mttt) cc_final: 0.7035 (mtpp)
REVERT: A  350 ASP cc_start: 0.7491 (t0) cc_final: 0.7233 (t0)
REVERT: A  368 ASP cc_start: 0.6833 (t70) cc_final: 0.6512 (t70)
REVERT: A  375 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6676 (mm-30)
REVERT: A  455 MET cc_start: 0.6945 (tmm) cc_final: 0.6714 (tmm)
REVERT: A  474 MET cc_start: 0.5066 (mmt) cc_final: 0.4172 (mmt)
REVERT: A  479 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6376 (tm-30)
REVERT: A  522 GLN cc_start: 0.7992 (pt0) cc_final: 0.7641 (pt0)
REVERT: A  552 GLN cc_start: 0.7918 (tp40) cc_final: 0.7650 (tp-100)
REVERT: A  559 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7159 (ptp90)
REVERT: A  564 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7041 (mm-30)
REVERT: A  571 GLU cc_start: 0.7759 (tp30) cc_final: 0.7530 (tp30)
REVERT: B  357 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.7827 (ttp-110)
REVERT: B  377 PHE cc_start: 0.8284 (t80) cc_final: 0.7931 (t80)
REVERT: B  511 VAL cc_start: 0.8444 (t) cc_final: 0.8069 (m)
REVERT: B  519 HIS cc_start: 0.6020 (m-70) cc_final: 0.5688 (m-70)
  outliers start: 22
  outliers final: 17
  residues processed: 198
  average time/residue: 0.0569
  time to fit residues: 15.3888
Evaluate side-chains
  191 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 173
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  302 TRP
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 25 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0370
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0980
   chunk 58 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0770
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.2616

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.128918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112987 restraints weight = 12947.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.116795 restraints weight = 5420.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.119279 restraints weight = 2896.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.120733 restraints weight = 1798.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.121819 restraints weight = 1291.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3409
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3409 r_free = 0.3409    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3409 r_free = 0.3409    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3409
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6463  Z= 0.143
  Angle     :  0.575   6.147   8791  Z= 0.297
  Chirality :  0.042   0.229    927
  Planarity :  0.004   0.037   1123
  Dihedral  :  4.733  38.802    953
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 24.55 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.31), residues: 750
  helix:  1.14 (0.26), residues: 381
  sheet: -0.10 (0.78), residues: 44
  loop : -0.50 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 460 
 TYR   0.022   0.001   TYR A  41 
 PHE   0.017   0.001   PHE A 369 
 TRP   0.013   0.001   TRP A 203 
 HIS   0.009   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 6453)
  covalent geometry    : angle       0.56500 /  0.29 ( 8765)
  SS BOND              : bond        0.00253 /  0.12 (    4)
  SS BOND              : angle       2.61904 /  1.34 (    8)
  hydrogen bonds       : bond        0.04586 /  3.23 (  299)
  hydrogen bonds       : angle       4.83739 /  3.61 (  863)
  link_NAG-ASN         : bond        0.00374 /  0.19 (    6)
  link_NAG-ASN         : angle       1.71952 /  1.05 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7226 (mt0) cc_final: 0.6927 (mt0)
REVERT: A   35 GLU cc_start: 0.6991 (tt0) cc_final: 0.6461 (mt-10)
REVERT: A   37 GLU cc_start: 0.7260 (tt0) cc_final: 0.6969 (tt0)
REVERT: A   61 ASN cc_start: 0.7714 (m-40) cc_final: 0.7403 (m110)
REVERT: A   87 GLU cc_start: 0.7471 (tp30) cc_final: 0.6980 (mp0)
REVERT: A  100 LEU cc_start: 0.8340 (tp) cc_final: 0.8051 (mt)
REVERT: A  152 MET cc_start: 0.6524 (mmm) cc_final: 0.5973 (mmm)
REVERT: A  185 VAL cc_start: 0.8420 (m) cc_final: 0.8157 (p)
REVERT: A  221 GLN cc_start: 0.7046 (tt0) cc_final: 0.6683 (tp40)
REVERT: A  288 LYS cc_start: 0.8567 (mmpt) cc_final: 0.8311 (mmtp)
REVERT: A  297 MET cc_start: 0.7859 (tpp) cc_final: 0.7655 (tpp)
REVERT: A  312 GLU cc_start: 0.6796 (tt0) cc_final: 0.6470 (tt0)
REVERT: A  313 LYS cc_start: 0.7446 (mttt) cc_final: 0.7003 (mtpp)
REVERT: A  350 ASP cc_start: 0.7503 (t0) cc_final: 0.7270 (t0)
REVERT: A  368 ASP cc_start: 0.6824 (t70) cc_final: 0.6505 (t70)
REVERT: A  375 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6632 (mm-30)
REVERT: A  440 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7730 (tt)
REVERT: A  455 MET cc_start: 0.6987 (tmm) cc_final: 0.6747 (tmm)
REVERT: A  472 GLN cc_start: 0.7094 (mt0) cc_final: 0.6740 (pt0)
REVERT: A  474 MET cc_start: 0.4997 (mmt) cc_final: 0.4743 (mmt)
REVERT: A  479 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6595 (tm-30)
REVERT: A  482 ARG cc_start: 0.7521 (mtt-85) cc_final: 0.7296 (mmt180)
REVERT: A  518 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7548 (tmm-80)
REVERT: A  559 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7180 (ptp90)
REVERT: A  564 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7086 (mm-30)
REVERT: A  571 GLU cc_start: 0.7756 (tp30) cc_final: 0.7524 (tp30)
REVERT: B  377 PHE cc_start: 0.8315 (t80) cc_final: 0.7926 (t80)
REVERT: B  458 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7932 (mmmt)
REVERT: B  511 VAL cc_start: 0.8446 (t) cc_final: 0.8051 (m)
  outliers start: 25
  outliers final: 16
  residues processed: 194
  average time/residue: 0.0515
  time to fit residues: 13.7167
Evaluate side-chains
  199 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  302 TRP
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  518 ARG
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  474 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 66 optimal weight:    0.1980
   chunk 46 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0040
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 2 optimal weight:    0.4980
   chunk 23 optimal weight:    0.2980
   overall best weight:    0.2792

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.127560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.111081 restraints weight = 14579.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.115100 restraints weight = 5877.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.117654 restraints weight = 3064.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.119294 restraints weight = 1885.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.120364 restraints weight = 1311.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6463  Z= 0.148
  Angle     :  0.587   6.931   8791  Z= 0.303
  Chirality :  0.041   0.233    927
  Planarity :  0.004   0.036   1123
  Dihedral  :  4.769  38.953    953
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 24.55 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.31), residues: 750
  helix:  1.11 (0.26), residues: 383
  sheet: -0.15 (0.77), residues: 44
  loop : -0.49 (0.37), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.022   0.001   TYR A  41 
 PHE   0.017   0.001   PHE A 369 
 TRP   0.016   0.001   TRP A 203 
 HIS   0.010   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.15 ( 6453)
  covalent geometry    : angle       0.57702 /  0.30 ( 8765)
  SS BOND              : bond        0.00302 /  0.15 (    4)
  SS BOND              : angle       2.56460 /  1.32 (    8)
  hydrogen bonds       : bond        0.04614 /  3.25 (  299)
  hydrogen bonds       : angle       4.89009 /  3.64 (  863)
  link_NAG-ASN         : bond        0.00373 /  0.19 (    6)
  link_NAG-ASN         : angle       1.77944 /  1.07 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 171
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7243 (mt0) cc_final: 0.6940 (mt0)
REVERT: A   35 GLU cc_start: 0.6988 (tt0) cc_final: 0.6466 (mt-10)
REVERT: A   37 GLU cc_start: 0.7243 (tt0) cc_final: 0.6964 (tt0)
REVERT: A   61 ASN cc_start: 0.7724 (m-40) cc_final: 0.7403 (m110)
REVERT: A   87 GLU cc_start: 0.7466 (tp30) cc_final: 0.6974 (mp0)
REVERT: A  152 MET cc_start: 0.6535 (mmm) cc_final: 0.6030 (mmm)
REVERT: A  185 VAL cc_start: 0.8411 (m) cc_final: 0.8152 (p)
REVERT: A  221 GLN cc_start: 0.7060 (tt0) cc_final: 0.6688 (tp40)
REVERT: A  288 LYS cc_start: 0.8563 (mmpt) cc_final: 0.8312 (mmtp)
REVERT: A  297 MET cc_start: 0.7879 (tpp) cc_final: 0.7671 (tpp)
REVERT: A  312 GLU cc_start: 0.6722 (tt0) cc_final: 0.6439 (tt0)
REVERT: A  313 LYS cc_start: 0.7399 (mttt) cc_final: 0.6974 (mtpp)
REVERT: A  350 ASP cc_start: 0.7502 (t0) cc_final: 0.7279 (t0)
REVERT: A  368 ASP cc_start: 0.6800 (t70) cc_final: 0.6478 (t70)
REVERT: A  375 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6628 (mm-30)
REVERT: A  440 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7815 (tp)
REVERT: A  455 MET cc_start: 0.7029 (tmm) cc_final: 0.6792 (tmm)
REVERT: A  472 GLN cc_start: 0.7058 (mt0) cc_final: 0.6706 (pt0)
REVERT: A  474 MET cc_start: 0.5023 (mmt) cc_final: 0.4752 (mmt)
REVERT: A  479 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6584 (tm-30)
REVERT: A  482 ARG cc_start: 0.7391 (mtt-85) cc_final: 0.7079 (mmt180)
REVERT: A  518 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7539 (tmm-80)
REVERT: A  559 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7184 (ptp90)
REVERT: A  564 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7094 (mm-30)
REVERT: A  571 GLU cc_start: 0.7745 (tp30) cc_final: 0.7518 (tp30)
REVERT: A  572 ASN cc_start: 0.7615 (t0) cc_final: 0.7337 (t0)
REVERT: B  458 LYS cc_start: 0.8273 (mmmt) cc_final: 0.7968 (mmmt)
REVERT: B  511 VAL cc_start: 0.8450 (t) cc_final: 0.8047 (m)
  outliers start: 27
  outliers final: 19
  residues processed: 188
  average time/residue: 0.0590
  time to fit residues: 14.9920
Evaluate side-chains
  197 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  302 TRP
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  518 ARG
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  474 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 50 optimal weight:    0.0970
   chunk 21 optimal weight:    0.9980
   chunk 14 optimal weight:    0.1980
   chunk 12 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0870
   chunk 22 optimal weight:    0.2980
   chunk 64 optimal weight:    0.3980
   overall best weight:    0.2156

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 GLN
A 345 HIS
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.125488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.108091 restraints weight = 18589.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.112448 restraints weight = 7126.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.115188 restraints weight = 3611.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.116934 restraints weight = 2192.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.118069 restraints weight = 1511.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3480
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3480 r_free = 0.3480    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3480
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6463  Z= 0.133
  Angle     :  0.588   7.267   8791  Z= 0.301
  Chirality :  0.041   0.233    927
  Planarity :  0.004   0.046   1123
  Dihedral  :  4.711  39.072    953
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 24.55 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.31), residues: 750
  helix:  1.16 (0.26), residues: 383
  sheet: -0.20 (0.77), residues: 44
  loop : -0.51 (0.37), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.022   0.001   TYR A  41 
 PHE   0.017   0.001   PHE A 369 
 TRP   0.013   0.001   TRP A 203 
 HIS   0.009   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 6453)
  covalent geometry    : angle       0.57843 /  0.30 ( 8765)
  SS BOND              : bond        0.00294 /  0.14 (    4)
  SS BOND              : angle       2.57392 /  1.32 (    8)
  hydrogen bonds       : bond        0.04523 /  3.19 (  299)
  hydrogen bonds       : angle       4.85016 /  3.61 (  863)
  link_NAG-ASN         : bond        0.00389 /  0.20 (    6)
  link_NAG-ASN         : angle       1.69652 /  1.02 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 172
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7202 (mt0) cc_final: 0.6909 (mt0)
REVERT: A   35 GLU cc_start: 0.6915 (tt0) cc_final: 0.6423 (mt-10)
REVERT: A   37 GLU cc_start: 0.7172 (tt0) cc_final: 0.6870 (tt0)
REVERT: A   61 ASN cc_start: 0.7692 (m-40) cc_final: 0.7400 (m110)
REVERT: A   87 GLU cc_start: 0.7417 (tp30) cc_final: 0.6945 (mp0)
REVERT: A  100 LEU cc_start: 0.8356 (tp) cc_final: 0.8027 (mt)
REVERT: A  152 MET cc_start: 0.6554 (mmm) cc_final: 0.6089 (mmm)
REVERT: A  185 VAL cc_start: 0.8420 (m) cc_final: 0.8156 (p)
REVERT: A  190 MET cc_start: 0.7400 (ttm) cc_final: 0.7151 (ttp)
REVERT: A  221 GLN cc_start: 0.7020 (tt0) cc_final: 0.6716 (tp40)
REVERT: A  288 LYS cc_start: 0.8581 (mmpt) cc_final: 0.8361 (mmtp)
REVERT: A  313 LYS cc_start: 0.7412 (mttt) cc_final: 0.6988 (mtpp)
REVERT: A  440 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7722 (tt)
REVERT: A  455 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6759 (tmm)
REVERT: A  472 GLN cc_start: 0.7069 (mt0) cc_final: 0.6750 (pt0)
REVERT: A  474 MET cc_start: 0.5015 (mmt) cc_final: 0.4759 (mmt)
REVERT: A  479 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6566 (tm-30)
REVERT: A  518 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7604 (tmm-80)
REVERT: A  559 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7162 (ptp90)
REVERT: A  564 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7023 (mm-30)
REVERT: A  572 ASN cc_start: 0.7563 (t0) cc_final: 0.7305 (t0)
REVERT: B  376 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7537 (p)
REVERT: B  458 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7927 (mmmt)
REVERT: B  511 VAL cc_start: 0.8462 (t) cc_final: 0.8079 (m)
  outliers start: 27
  outliers final: 19
  residues processed: 188
  average time/residue: 0.0565
  time to fit residues: 14.4293
Evaluate side-chains
  198 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  302 TRP
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  518 ARG
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  493 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0470
   chunk 36 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   chunk 34 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.4078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.122631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.107933 restraints weight = 10295.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.111236 restraints weight = 4715.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.113311 restraints weight = 2671.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.114703 restraints weight = 1759.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115432 restraints weight = 1293.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6463  Z= 0.190
  Angle     :  0.640   7.359   8791  Z= 0.329
  Chirality :  0.043   0.259    927
  Planarity :  0.004   0.037   1123
  Dihedral  :  4.946  39.220    953
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 24.85 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.31), residues: 750
  helix:  0.95 (0.26), residues: 384
  sheet: -0.22 (0.77), residues: 44
  loop : -0.49 (0.37), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 460 
 TYR   0.023   0.001   TYR A  41 
 PHE   0.018   0.001   PHE A 369 
 TRP   0.017   0.002   TRP B 452 
 HIS   0.011   0.002   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.19 ( 6453)
  covalent geometry    : angle       0.63030 /  0.33 ( 8765)
  SS BOND              : bond        0.00405 /  0.20 (    4)
  SS BOND              : angle       2.59432 /  1.35 (    8)
  hydrogen bonds       : bond        0.05020 /  3.55 (  299)
  hydrogen bonds       : angle       4.94054 /  3.66 (  863)
  link_NAG-ASN         : bond        0.00389 /  0.20 (    6)
  link_NAG-ASN         : angle       1.86624 /  1.17 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7250 (mt0) cc_final: 0.7033 (mt0)
REVERT: A   35 GLU cc_start: 0.6998 (tt0) cc_final: 0.6744 (mt-10)
REVERT: A   37 GLU cc_start: 0.7273 (tt0) cc_final: 0.6991 (tt0)
REVERT: A   61 ASN cc_start: 0.7710 (m-40) cc_final: 0.7401 (m110)
REVERT: A   87 GLU cc_start: 0.7424 (tp30) cc_final: 0.6962 (mp0)
REVERT: A  152 MET cc_start: 0.6716 (mmm) cc_final: 0.6194 (mmm)
REVERT: A  185 VAL cc_start: 0.8427 (m) cc_final: 0.8145 (p)
REVERT: A  204 ARG cc_start: 0.7462 (mtm180) cc_final: 0.6878 (mtm110)
REVERT: A  221 GLN cc_start: 0.7102 (tt0) cc_final: 0.6841 (tt0)
REVERT: A  288 LYS cc_start: 0.8595 (mmpt) cc_final: 0.8383 (mmtp)
REVERT: A  297 MET cc_start: 0.7845 (tpp) cc_final: 0.7609 (tpp)
REVERT: A  313 LYS cc_start: 0.7532 (mttt) cc_final: 0.7079 (mtpp)
REVERT: A  375 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6453 (mm-30)
REVERT: A  455 MET cc_start: 0.7003 (tmm) cc_final: 0.6723 (tmm)
REVERT: A  470 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7526 (tttm)
REVERT: A  474 MET cc_start: 0.4926 (mmt) cc_final: 0.4661 (mmt)
REVERT: A  479 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6411 (tm-30)
REVERT: A  559 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7194 (ptp90)
REVERT: A  564 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7093 (mm-30)
REVERT: A  572 ASN cc_start: 0.7585 (t0) cc_final: 0.7327 (t0)
REVERT: B  376 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7531 (p)
REVERT: B  458 LYS cc_start: 0.8312 (mmmt) cc_final: 0.8047 (mmmt)
REVERT: B  511 VAL cc_start: 0.8468 (t) cc_final: 0.8062 (m)
  outliers start: 25
  outliers final: 18
  residues processed: 199
  average time/residue: 0.0606
  time to fit residues: 16.3641
Evaluate side-chains
  199 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  302 TRP
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  474 GLN
Chi-restraints excluded: chain B residue  493 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 28 optimal weight:    0.0970
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0020
   chunk 73 optimal weight:    0.0870
   chunk 19 optimal weight:    0.2980
   chunk 60 optimal weight:    0.4980
   chunk 51 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.1364

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 345 HIS
A 526 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.126313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.108285 restraints weight = 21563.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112994 restraints weight = 7821.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.115872 restraints weight = 3826.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.117747 restraints weight = 2257.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118952 restraints weight = 1519.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6463  Z= 0.126
  Angle     :  0.608   7.140   8791  Z= 0.313
  Chirality :  0.041   0.230    927
  Planarity :  0.004   0.036   1123
  Dihedral  :  4.740  39.986    953
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 26.65 %
    Favored  : 70.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.31), residues: 750
  helix:  1.00 (0.26), residues: 386
  sheet: -0.28 (0.76), residues: 44
  loop : -0.40 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 460 
 TYR   0.020   0.001   TYR A  41 
 PHE   0.016   0.001   PHE A 369 
 TRP   0.022   0.001   TRP A  69 
 HIS   0.010   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 ( 6453)
  covalent geometry    : angle       0.60024 /  0.31 ( 8765)
  SS BOND              : bond        0.00318 /  0.15 (    4)
  SS BOND              : angle       2.42744 /  1.25 (    8)
  hydrogen bonds       : bond        0.04518 /  3.19 (  299)
  hydrogen bonds       : angle       4.86675 /  3.62 (  863)
  link_NAG-ASN         : bond        0.00411 /  0.21 (    6)
  link_NAG-ASN         : angle       1.56691 /  0.97 (   18)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 GLN cc_start: 0.7256 (mt0) cc_final: 0.7011 (mt0)
REVERT: A   35 GLU cc_start: 0.6949 (tt0) cc_final: 0.6663 (mt-10)
REVERT: A   37 GLU cc_start: 0.7177 (tt0) cc_final: 0.6875 (tt0)
REVERT: A   61 ASN cc_start: 0.7744 (m-40) cc_final: 0.7420 (m110)
REVERT: A   81 GLN cc_start: 0.6954 (tt0) cc_final: 0.6674 (tm-30)
REVERT: A  152 MET cc_start: 0.6662 (mmm) cc_final: 0.6070 (mmm)
REVERT: A  185 VAL cc_start: 0.8399 (m) cc_final: 0.8137 (p)
REVERT: A  190 MET cc_start: 0.7464 (ttm) cc_final: 0.7202 (ttp)
REVERT: A  204 ARG cc_start: 0.7396 (mtm180) cc_final: 0.6781 (mtm110)
REVERT: A  221 GLN cc_start: 0.6977 (tt0) cc_final: 0.6640 (tt0)
REVERT: A  288 LYS cc_start: 0.8553 (mmpt) cc_final: 0.8329 (mmtp)
REVERT: A  313 LYS cc_start: 0.7440 (mttt) cc_final: 0.6977 (mtpp)
REVERT: A  375 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6419 (mm-30)
REVERT: A  455 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6800 (tmm)
REVERT: A  470 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7542 (tttm)
REVERT: A  479 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6572 (tm-30)
REVERT: A  489 GLU cc_start: 0.6897 (pm20) cc_final: 0.6606 (pm20)
REVERT: A  559 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7148 (ptp90)
REVERT: A  564 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7029 (mm-30)
REVERT: B  376 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7532 (p)
REVERT: B  401 VAL cc_start: 0.8635 (p) cc_final: 0.8408 (m)
REVERT: B  403 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8316 (mtmt)
REVERT: B  438 SER cc_start: 0.8651 (p) cc_final: 0.8353 (p)
REVERT: B  455 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7509 (mt)
REVERT: B  458 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7925 (mmmt)
REVERT: B  511 VAL cc_start: 0.8455 (t) cc_final: 0.8085 (m)
  outliers start: 16
  outliers final: 10
  residues processed: 192
  average time/residue: 0.0519
  time to fit residues: 13.7752
Evaluate side-chains
  183 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 169
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  435 GLU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  474 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0870
   chunk 57 optimal weight:    0.4980
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0980
   chunk 62 optimal weight:    0.0000
   chunk 35 optimal weight:    0.0020
   chunk 33 optimal weight:    0.6980
   chunk 43 optimal weight:    0.3980
   chunk 19 optimal weight:    0.3980
   overall best weight:    0.1170

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 345 HIS
A 526 GLN
A 599 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.109681 restraints weight = 18626.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.114132 restraints weight = 7170.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.116856 restraints weight = 3613.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.118660 restraints weight = 2177.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.119819 restraints weight = 1490.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6463  Z= 0.125
  Angle     :  0.600   7.091   8791  Z= 0.308
  Chirality :  0.041   0.221    927
  Planarity :  0.004   0.036   1123
  Dihedral  :  4.601  38.977    953
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 26.65 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.31), residues: 750
  helix:  1.07 (0.26), residues: 387
  sheet: -0.31 (0.75), residues: 44
  loop : -0.35 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 204 
 TYR   0.019   0.001   TYR A  41 
 PHE   0.018   0.001   PHE A 369 
 TRP   0.019   0.001   TRP A  69 
 HIS   0.010   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 6453)
  covalent geometry    : angle       0.59294 /  0.31 ( 8765)
  SS BOND              : bond        0.00330 /  0.16 (    4)
  SS BOND              : angle       2.35425 /  1.22 (    8)
  hydrogen bonds       : bond        0.04468 /  3.16 (  299)
  hydrogen bonds       : angle       4.81772 /  3.58 (  863)
  link_NAG-ASN         : bond        0.00394 /  0.20 (    6)
  link_NAG-ASN         : angle       1.51482 /  0.93 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1186.26 seconds
wall clock time: 21 minutes 2.76 seconds (1262.76 seconds total)