Starting phenix.real_space_refine
on Tue Mar  3 15:45:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tew_25853/03_2026/7tew_25853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tew_25853/03_2026/7tew_25853.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tew_25853/03_2026/7tew_25853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tew_25853/03_2026/7tew_25853.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tew_25853/03_2026/7tew_25853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tew_25853/03_2026/7tew_25853.map"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4188      2.51       5
     N    1082      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6555
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1595
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      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: 1.35, per 1000 atoms: 0.21
  Number of scatterers: 6555
  At special positions: 0
  Unit cell: (80, 86, 122, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1248      8.00
     N    1082      7.00
     C    4188      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 542 " 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 B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 202.0 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 7 sheets defined
      57.0% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.752A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 4.114A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LEU E  39 " --> pdb=" O   GLU E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
    Processing helix  chain 'E' and resid 82 through 83
      No H-bonds generated for 'chain 'E' and resid 82 through 83'
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.753A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.041A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 146 through 155
      removed outlier: 4.045A  pdb=" N   ILE E 151 " --> pdb=" O   GLY E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.697A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 220 through 252
      removed outlier: 3.928A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.811A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 300
    Processing helix  chain 'E' and resid 303 through 319
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.521A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.689A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.289A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
      removed outlier: 3.511A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.328A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.648A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 513 through 533
      removed outlier: 3.614A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.896A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 4.002A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132
      removed outlier: 3.774A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 6.158A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.347A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    915 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2087
        1.35 -     1.47: 1795
        1.47 -     1.60: 2797
        1.60 -     1.73: 0
        1.73 -     1.85: 58
  Bond restraints: 6737
  Sorted by residual:
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.462 -0.056 2.00e-02 2.50e+03 7.80e+00
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.22e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 5.99e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.19e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.15e+00
  ... (remaining 6732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 8757
        1.91 -     3.82: 350
        3.82 -     5.73: 34
        5.73 -     7.63: 8
        7.63 -     9.54: 4
  Bond angle restraints: 9153
  Sorted by residual:
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.24   -5.88 1.42e+00 4.96e-01 1.71e+01
  angle pdb=" CA  CYS E 141 "
        pdb=" CB  CYS E 141 "
        pdb=" SG  CYS E 141 "
      ideal   model   delta    sigma   weight residual
     114.40  122.95   -8.55 2.30e+00 1.89e-01 1.38e+01
  angle pdb=" C   HIS E  34 "
        pdb=" N   GLU E  35 "
        pdb=" CA  GLU E  35 "
      ideal   model   delta    sigma   weight residual
     122.38  115.72    6.66 1.81e+00 3.05e-01 1.35e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  116.25   -3.65 1.00e+00 1.00e+00 1.33e+01
  angle pdb=" CA  LYS E  31 "
        pdb=" CB  LYS E  31 "
        pdb=" CG  LYS E  31 "
      ideal   model   delta    sigma   weight residual
     114.10  120.85   -6.75 2.00e+00 2.50e-01 1.14e+01
  ... (remaining 9148 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 3680
       16.87 -    33.74: 316
       33.74 -    50.61: 51
       50.61 -    67.47: 12
       67.47 -    84.34: 12
  Dihedral angle restraints: 4071
    sinusoidal: 1733
      harmonic: 2338
  Sorted by residual:
  dihedral pdb=" CB  CYS E 133 "
           pdb=" SG  CYS E 133 "
           pdb=" SG  CYS E 141 "
           pdb=" CB  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -47.25  -38.75     1      1.00e+01 1.00e-02 2.11e+01
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   14.06   64.94     1      2.00e+01 2.50e-03 1.38e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.88    8.28     0      2.50e+00 1.60e-01 1.10e+01
  ... (remaining 4068 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 729
       0.056 -    0.111: 186
       0.111 -    0.166: 51
       0.166 -    0.222: 8
       0.222 -    0.277: 2
  Chirality restraints: 976
  Sorted by residual:
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" C1  NAG E 703 "
            pdb=" ND2 ASN E 103 "
            pdb=" C2  NAG E 703 "
            pdb=" O5  NAG E 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 973 not shown)

  Planarity restraints: 1185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.052 5.00e-02 4.00e+02   7.79e-02 9.70e+00
        pdb=" N   PRO E 590 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 499 "   -0.048 5.00e-02 4.00e+02   7.10e-02 8.06e+00
        pdb=" N   PRO E 500 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO E 500 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 500 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "   -0.021 2.00e-02 2.50e+03   1.86e-02 6.95e+00
        pdb=" CG  TYR B 495 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1182 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.86: 2224
        2.86 -     3.37: 5996
        3.37 -     3.88: 11266
        3.88 -     4.39: 12492
        4.39 -     4.90: 21655
  Nonbonded interactions: 53633
  Sorted by model distance:
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" O   SER E  47 "
            pdb=" ND2 ASN E  51 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.387 3.120
  ... (remaining 53628 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             5.660
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.730
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   6750  Z= 0.234
  Angle     :  0.878  11.268   9186  Z= 0.493
  Chirality :  0.057   0.277    976
  Planarity :  0.008   0.078   1178
  Dihedral  : 13.336  84.341   2553
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.29 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.00 (0.25), residues: 793
  helix:  0.53 (0.22), residues: 392
  sheet:  0.98 (0.72), residues: 43
  loop : -0.64 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 460 
 TYR   0.045   0.003   TYR B 495 
 PHE   0.027   0.003   PHE E 369 
 TRP   0.020   0.002   TRP E  69 
 HIS   0.011   0.002   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 6737)
  covalent geometry    : angle       0.85235 ( 9153)
  SS BOND              : bond        0.00530 (    6)
  SS BOND              : angle       2.60855 (   12)
  hydrogen bonds       : bond        0.14790 (  322)
  hydrogen bonds       : angle       6.02989 (  915)
  link_NAG-ASN         : bond        0.00675 (    7)
  link_NAG-ASN         : angle       4.09989 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8482 (ttpt)
REVERT: B  424 LYS cc_start: 0.8692 (tptt) cc_final: 0.8170 (tppt)
REVERT: B  448 ASN cc_start: 0.9203 (t0) cc_final: 0.8699 (t0)
REVERT: B  458 LYS cc_start: 0.9307 (mtmt) cc_final: 0.9071 (mtmm)
REVERT: B  467 ASP cc_start: 0.8431 (t0) cc_final: 0.8106 (t0)
REVERT: B  473 TYR cc_start: 0.9316 (t80) cc_final: 0.9062 (t80)
REVERT: B  474 GLN cc_start: 0.8885 (tt0) cc_final: 0.8616 (tt0)
REVERT: E  108 LEU cc_start: 0.8613 (tp) cc_final: 0.8360 (tp)
REVERT: E  249 MET cc_start: 0.8484 (ttm) cc_final: 0.8082 (mtp)
REVERT: E  297 MET cc_start: 0.9202 (mtm) cc_final: 0.8995 (mtm)
REVERT: E  302 TRP cc_start: 0.8366 (m-10) cc_final: 0.7320 (m100)
REVERT: E  498 CYS cc_start: 0.8204 (t) cc_final: 0.7637 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1101
  time to fit residues: 18.5839
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.066265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.052736 restraints weight = 26598.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.054825 restraints weight = 13059.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.056213 restraints weight = 8265.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.057145 restraints weight = 6056.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.057701 restraints weight = 4871.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6750  Z= 0.138
  Angle     :  0.571   6.427   9186  Z= 0.295
  Chirality :  0.040   0.145    976
  Planarity :  0.005   0.049   1178
  Dihedral  :  5.283  52.851   1013
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  8.29 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.28), residues: 793
  helix:  1.43 (0.25), residues: 406
  sheet:  1.12 (0.76), residues: 42
  loop : -0.10 (0.30), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 452 
 TYR   0.013   0.001   TYR B 453 
 PHE   0.015   0.001   PHE E 428 
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6737)
  covalent geometry    : angle       0.55355 ( 9153)
  SS BOND              : bond        0.00352 (    6)
  SS BOND              : angle       1.84806 (   12)
  hydrogen bonds       : bond        0.04251 (  322)
  hydrogen bonds       : angle       4.57953 (  915)
  link_NAG-ASN         : bond        0.00329 (    7)
  link_NAG-ASN         : angle       2.62105 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  424 LYS cc_start: 0.8713 (tptt) cc_final: 0.8322 (tppt)
REVERT: B  448 ASN cc_start: 0.9187 (t0) cc_final: 0.8824 (t0)
REVERT: B  458 LYS cc_start: 0.9296 (mtmt) cc_final: 0.9065 (mtmm)
REVERT: B  467 ASP cc_start: 0.8205 (t0) cc_final: 0.7910 (t0)
REVERT: E  108 LEU cc_start: 0.8514 (tp) cc_final: 0.8146 (tp)
REVERT: E  232 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8808 (mp0)
REVERT: E  302 TRP cc_start: 0.8420 (m-10) cc_final: 0.7625 (m100)
REVERT: E  366 MET cc_start: 0.8960 (mtp) cc_final: 0.8682 (mtm)
REVERT: E  498 CYS cc_start: 0.8467 (t) cc_final: 0.8097 (t)
  outliers start: 13
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0818
  time to fit residues: 8.9187
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue  447 VAL
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.064655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.051434 restraints weight = 26302.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.053406 restraints weight = 12956.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.054736 restraints weight = 8287.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.055644 restraints weight = 6077.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.056248 restraints weight = 4908.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6750  Z= 0.129
  Angle     :  0.528   5.765   9186  Z= 0.270
  Chirality :  0.040   0.137    976
  Planarity :  0.004   0.046   1178
  Dihedral  :  4.935  53.860   1013
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.00 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.29), residues: 793
  helix:  1.65 (0.26), residues: 413
  sheet:  0.86 (0.75), residues: 41
  loop :  0.11 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 403 
 TYR   0.021   0.001   TYR E 613 
 PHE   0.013   0.001   PHE E 369 
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6737)
  covalent geometry    : angle       0.51590 ( 9153)
  SS BOND              : bond        0.00433 (    6)
  SS BOND              : angle       1.71293 (   12)
  hydrogen bonds       : bond        0.03847 (  322)
  hydrogen bonds       : angle       4.41967 (  915)
  link_NAG-ASN         : bond        0.00314 (    7)
  link_NAG-ASN         : angle       2.06232 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7832 (ptmm)
REVERT: B  409 GLN cc_start: 0.9291 (mt0) cc_final: 0.8957 (tt0)
REVERT: B  448 ASN cc_start: 0.9236 (t0) cc_final: 0.8854 (t0)
REVERT: B  458 LYS cc_start: 0.9312 (mtmt) cc_final: 0.9108 (mtmm)
REVERT: B  467 ASP cc_start: 0.8285 (t0) cc_final: 0.7936 (t0)
REVERT: E   62 MET cc_start: 0.9467 (OUTLIER) cc_final: 0.9112 (mtm)
REVERT: E  108 LEU cc_start: 0.8525 (tp) cc_final: 0.8122 (tp)
REVERT: E  232 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8818 (mp0)
REVERT: E  267 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9264 (mm)
REVERT: E  302 TRP cc_start: 0.8458 (m-10) cc_final: 0.7739 (m100)
REVERT: E  366 MET cc_start: 0.8999 (mtp) cc_final: 0.8690 (mtm)
REVERT: E  435 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8641 (mp0)
REVERT: E  498 CYS cc_start: 0.8672 (t) cc_final: 0.8340 (t)
  outliers start: 14
  outliers final: 7
  residues processed: 73
  average time/residue: 0.0806
  time to fit residues: 8.0971
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  386 LYS
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 39 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.063405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.049491 restraints weight = 27327.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.051518 restraints weight = 13574.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.052812 restraints weight = 8729.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.053695 restraints weight = 6517.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.054189 restraints weight = 5335.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6750  Z= 0.154
  Angle     :  0.527   5.756   9186  Z= 0.270
  Chirality :  0.040   0.138    976
  Planarity :  0.004   0.043   1178
  Dihedral  :  4.927  54.699   1013
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 10.00 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.29), residues: 793
  helix:  1.69 (0.26), residues: 415
  sheet:  0.78 (0.76), residues: 41
  loop :  0.17 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 169 
 TYR   0.017   0.001   TYR B 473 
 PHE   0.014   0.001   PHE E 369 
 TRP   0.016   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6737)
  covalent geometry    : angle       0.51761 ( 9153)
  SS BOND              : bond        0.00489 (    6)
  SS BOND              : angle       1.57175 (   12)
  hydrogen bonds       : bond        0.03816 (  322)
  hydrogen bonds       : angle       4.38352 (  915)
  link_NAG-ASN         : bond        0.00269 (    7)
  link_NAG-ASN         : angle       1.85113 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  448 ASN cc_start: 0.9212 (t0) cc_final: 0.8794 (t0)
REVERT: B  467 ASP cc_start: 0.8203 (t0) cc_final: 0.7875 (t0)
REVERT: E   62 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.8993 (mtm)
REVERT: E  108 LEU cc_start: 0.8527 (tp) cc_final: 0.8128 (tp)
REVERT: E  208 GLU cc_start: 0.8759 (tt0) cc_final: 0.8491 (tt0)
REVERT: E  232 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8826 (mp0)
REVERT: E  249 MET cc_start: 0.8610 (mtp) cc_final: 0.8332 (mtt)
REVERT: E  277 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8582 (t0)
REVERT: E  366 MET cc_start: 0.9007 (mtp) cc_final: 0.8684 (mtm)
REVERT: E  435 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8696 (mp0)
REVERT: E  498 CYS cc_start: 0.9046 (t) cc_final: 0.8619 (t)
  outliers start: 16
  outliers final: 8
  residues processed: 68
  average time/residue: 0.0778
  time to fit residues: 7.3616
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 4 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
E 277 ASN
E 522 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.061181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.047706 restraints weight = 27645.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.049645 restraints weight = 13507.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.050902 restraints weight = 8587.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.051770 restraints weight = 6353.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.052361 restraints weight = 5155.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6750  Z= 0.223
  Angle     :  0.579   5.923   9186  Z= 0.298
  Chirality :  0.042   0.145    976
  Planarity :  0.004   0.044   1178
  Dihedral  :  5.221  54.843   1013
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 11.14 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.30), residues: 793
  helix:  1.71 (0.26), residues: 408
  sheet:  0.16 (0.66), residues: 53
  loop :  0.31 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 403 
 TYR   0.017   0.001   TYR B 453 
 PHE   0.016   0.002   PHE E 369 
 TRP   0.015   0.002   TRP E 302 
 HIS   0.006   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 6737)
  covalent geometry    : angle       0.57038 ( 9153)
  SS BOND              : bond        0.00481 (    6)
  SS BOND              : angle       1.54012 (   12)
  hydrogen bonds       : bond        0.04093 (  322)
  hydrogen bonds       : angle       4.49262 (  915)
  link_NAG-ASN         : bond        0.00245 (    7)
  link_NAG-ASN         : angle       1.82956 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  424 LYS cc_start: 0.8837 (tptt) cc_final: 0.8385 (tppt)
REVERT: B  448 ASN cc_start: 0.9235 (t0) cc_final: 0.8842 (t0)
REVERT: B  467 ASP cc_start: 0.8175 (t0) cc_final: 0.7819 (t0)
REVERT: E   62 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.9014 (mtm)
REVERT: E  108 LEU cc_start: 0.8501 (tp) cc_final: 0.8126 (tp)
REVERT: E  208 GLU cc_start: 0.8780 (tt0) cc_final: 0.8526 (tm-30)
REVERT: E  249 MET cc_start: 0.8712 (mtp) cc_final: 0.8159 (mtm)
REVERT: E  277 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8708 (t0)
REVERT: E  323 MET cc_start: 0.9582 (mmp) cc_final: 0.8937 (mmp)
REVERT: E  366 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8743 (mtp)
REVERT: E  435 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8622 (mp0)
REVERT: E  498 CYS cc_start: 0.9059 (t) cc_final: 0.8808 (t)
  outliers start: 20
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0759
  time to fit residues: 6.7333
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  480 MET
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.062364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.048918 restraints weight = 27378.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.050871 restraints weight = 13335.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.052149 restraints weight = 8487.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.053016 restraints weight = 6255.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.053615 restraints weight = 5085.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6750  Z= 0.129
  Angle     :  0.516   5.547   9186  Z= 0.263
  Chirality :  0.040   0.133    976
  Planarity :  0.004   0.043   1178
  Dihedral  :  4.914  55.560   1013
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.00 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.30), residues: 793
  helix:  1.77 (0.26), residues: 407
  sheet:  0.10 (0.67), residues: 53
  loop :  0.36 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 452 
 TYR   0.011   0.001   TYR B 453 
 PHE   0.013   0.001   PHE E 369 
 TRP   0.012   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6737)
  covalent geometry    : angle       0.50759 ( 9153)
  SS BOND              : bond        0.00387 (    6)
  SS BOND              : angle       1.44782 (   12)
  hydrogen bonds       : bond        0.03697 (  322)
  hydrogen bonds       : angle       4.32891 (  915)
  link_NAG-ASN         : bond        0.00243 (    7)
  link_NAG-ASN         : angle       1.69814 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: B  424 LYS cc_start: 0.8848 (tptt) cc_final: 0.8405 (tppt)
REVERT: B  444 LYS cc_start: 0.9109 (ptpp) cc_final: 0.8903 (ptpp)
REVERT: B  467 ASP cc_start: 0.8054 (t0) cc_final: 0.7713 (t0)
REVERT: E   62 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.9035 (mtm)
REVERT: E  208 GLU cc_start: 0.8802 (tt0) cc_final: 0.8551 (tm-30)
REVERT: E  277 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8763 (t0)
REVERT: E  323 MET cc_start: 0.9591 (mmp) cc_final: 0.8902 (mmp)
REVERT: E  366 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8720 (mtp)
REVERT: E  435 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8672 (mp0)
REVERT: E  498 CYS cc_start: 0.9164 (t) cc_final: 0.8665 (t)
  outliers start: 15
  outliers final: 6
  residues processed: 62
  average time/residue: 0.0892
  time to fit residues: 7.4448
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 60 optimal weight:    0.3980
   chunk 59 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
E 277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.061373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.047884 restraints weight = 27091.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.049773 restraints weight = 13664.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.051018 restraints weight = 8858.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.051847 restraints weight = 6621.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.052373 restraints weight = 5424.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6750  Z= 0.169
  Angle     :  0.548   6.479   9186  Z= 0.279
  Chirality :  0.040   0.133    976
  Planarity :  0.004   0.042   1178
  Dihedral  :  4.984  55.646   1013
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.00 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.30), residues: 793
  helix:  1.81 (0.26), residues: 404
  sheet:  0.09 (0.68), residues: 53
  loop :  0.39 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 219 
 TYR   0.022   0.001   TYR B 473 
 PHE   0.014   0.001   PHE E 369 
 TRP   0.013   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6737)
  covalent geometry    : angle       0.53980 ( 9153)
  SS BOND              : bond        0.00421 (    6)
  SS BOND              : angle       1.51182 (   12)
  hydrogen bonds       : bond        0.03783 (  322)
  hydrogen bonds       : angle       4.34448 (  915)
  link_NAG-ASN         : bond        0.00239 (    7)
  link_NAG-ASN         : angle       1.70991 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  417 LYS cc_start: 0.9382 (mmmt) cc_final: 0.8979 (mmmt)
REVERT: B  424 LYS cc_start: 0.8861 (tptt) cc_final: 0.8430 (tppt)
REVERT: B  467 ASP cc_start: 0.8080 (t0) cc_final: 0.7795 (t0)
REVERT: E   62 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.9028 (mtm)
REVERT: E  208 GLU cc_start: 0.8805 (tt0) cc_final: 0.8562 (tm-30)
REVERT: E  277 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.8783 (t0)
REVERT: E  323 MET cc_start: 0.9593 (mmp) cc_final: 0.8890 (mmp)
REVERT: E  366 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8702 (mtp)
REVERT: E  435 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8626 (mp0)
REVERT: E  498 CYS cc_start: 0.9200 (t) cc_final: 0.8830 (t)
  outliers start: 16
  outliers final: 8
  residues processed: 59
  average time/residue: 0.0861
  time to fit residues: 6.7862
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.062023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.048306 restraints weight = 27250.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.050226 restraints weight = 13809.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.051476 restraints weight = 9004.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.052335 restraints weight = 6750.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.052903 restraints weight = 5536.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6750  Z= 0.133
  Angle     :  0.524   6.738   9186  Z= 0.266
  Chirality :  0.040   0.133    976
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.859  55.877   1013
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.29 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.30), residues: 793
  helix:  1.79 (0.26), residues: 406
  sheet:  0.12 (0.69), residues: 53
  loop :  0.42 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 452 
 TYR   0.019   0.001   TYR B 473 
 PHE   0.012   0.001   PHE E 369 
 TRP   0.011   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6737)
  covalent geometry    : angle       0.51654 ( 9153)
  SS BOND              : bond        0.00373 (    6)
  SS BOND              : angle       1.45502 (   12)
  hydrogen bonds       : bond        0.03626 (  322)
  hydrogen bonds       : angle       4.28234 (  915)
  link_NAG-ASN         : bond        0.00243 (    7)
  link_NAG-ASN         : angle       1.66432 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  424 LYS cc_start: 0.8869 (tptt) cc_final: 0.8432 (tppt)
REVERT: B  467 ASP cc_start: 0.8027 (t0) cc_final: 0.7753 (t0)
REVERT: E   62 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.9029 (mtm)
REVERT: E  208 GLU cc_start: 0.8806 (tt0) cc_final: 0.8552 (tm-30)
REVERT: E  277 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8859 (t0)
REVERT: E  323 MET cc_start: 0.9591 (mmp) cc_final: 0.8997 (mmp)
REVERT: E  366 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8750 (mtp)
REVERT: E  435 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8658 (mp0)
REVERT: E  498 CYS cc_start: 0.9175 (t) cc_final: 0.8677 (t)
  outliers start: 17
  outliers final: 10
  residues processed: 61
  average time/residue: 0.0921
  time to fit residues: 7.6378
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 334 ASN
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.059988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.046484 restraints weight = 27937.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.048396 restraints weight = 13683.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.049649 restraints weight = 8744.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.050498 restraints weight = 6482.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.051047 restraints weight = 5284.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6750  Z= 0.226
  Angle     :  0.592   6.722   9186  Z= 0.302
  Chirality :  0.042   0.141    976
  Planarity :  0.004   0.043   1178
  Dihedral  :  5.207  55.420   1013
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.71 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.30), residues: 793
  helix:  1.73 (0.26), residues: 407
  sheet: -0.02 (0.68), residues: 51
  loop :  0.43 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 403 
 TYR   0.017   0.002   TYR B 473 
 PHE   0.016   0.002   PHE E 369 
 TRP   0.014   0.001   TRP E 302 
 HIS   0.005   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 6737)
  covalent geometry    : angle       0.58501 ( 9153)
  SS BOND              : bond        0.00494 (    6)
  SS BOND              : angle       1.44575 (   12)
  hydrogen bonds       : bond        0.04014 (  322)
  hydrogen bonds       : angle       4.46779 (  915)
  link_NAG-ASN         : bond        0.00263 (    7)
  link_NAG-ASN         : angle       1.78715 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  424 LYS cc_start: 0.8924 (tptt) cc_final: 0.8497 (tppt)
REVERT: B  467 ASP cc_start: 0.8107 (t0) cc_final: 0.7852 (t0)
REVERT: E   62 MET cc_start: 0.9433 (mtp) cc_final: 0.9008 (mtm)
REVERT: E  208 GLU cc_start: 0.8817 (tt0) cc_final: 0.8599 (tm-30)
REVERT: E  277 ASN cc_start: 0.9314 (OUTLIER) cc_final: 0.8854 (t0)
REVERT: E  323 MET cc_start: 0.9606 (mmp) cc_final: 0.9383 (mmp)
REVERT: E  366 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8686 (mtp)
REVERT: E  498 CYS cc_start: 0.9227 (t) cc_final: 0.8907 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 61
  average time/residue: 0.0917
  time to fit residues: 7.4291
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   21 ILE
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0370
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0370
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.062517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.048815 restraints weight = 27081.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.050715 restraints weight = 13795.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.051990 restraints weight = 9025.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.052828 restraints weight = 6772.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.053428 restraints weight = 5569.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6750  Z= 0.107
  Angle     :  0.525   7.385   9186  Z= 0.264
  Chirality :  0.039   0.135    976
  Planarity :  0.003   0.041   1178
  Dihedral  :  4.781  56.089   1013
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.43 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.30), residues: 793
  helix:  1.81 (0.26), residues: 407
  sheet:  0.00 (0.69), residues: 53
  loop :  0.49 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 457 
 TYR   0.018   0.001   TYR B 473 
 PHE   0.011   0.001   PHE E 369 
 TRP   0.010   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6737)
  covalent geometry    : angle       0.51663 ( 9153)
  SS BOND              : bond        0.00328 (    6)
  SS BOND              : angle       1.43693 (   12)
  hydrogen bonds       : bond        0.03498 (  322)
  hydrogen bonds       : angle       4.25257 (  915)
  link_NAG-ASN         : bond        0.00282 (    7)
  link_NAG-ASN         : angle       1.70321 (   21)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  417 LYS cc_start: 0.9336 (mmmt) cc_final: 0.8991 (mmmt)
REVERT: B  424 LYS cc_start: 0.8839 (tptt) cc_final: 0.8439 (tppt)
REVERT: B  467 ASP cc_start: 0.8020 (t0) cc_final: 0.7718 (t0)
REVERT: E   62 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.9085 (mtm)
REVERT: E  208 GLU cc_start: 0.8838 (tt0) cc_final: 0.8593 (tm-30)
REVERT: E  277 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8926 (t0)
REVERT: E  323 MET cc_start: 0.9526 (mmp) cc_final: 0.9323 (mmp)
REVERT: E  498 CYS cc_start: 0.9167 (t) cc_final: 0.8616 (t)
  outliers start: 9
  outliers final: 5
  residues processed: 56
  average time/residue: 0.0810
  time to fit residues: 6.2735
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   62 MET
Chi-restraints excluded: chain E residue  277 ASN
Chi-restraints excluded: chain E residue  435 GLU
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  527 GLU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.061995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.048337 restraints weight = 27298.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.050235 restraints weight = 13848.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.051523 restraints weight = 9035.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.052382 restraints weight = 6731.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.052925 restraints weight = 5515.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6750  Z= 0.127
  Angle     :  0.536   7.369   9186  Z= 0.269
  Chirality :  0.040   0.129    976
  Planarity :  0.004   0.041   1178
  Dihedral  :  4.754  56.004   1013
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.29 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.30), residues: 793
  helix:  1.83 (0.26), residues: 405
  sheet:  0.04 (0.69), residues: 53
  loop :  0.53 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 460 
 TYR   0.017   0.001   TYR B 473 
 PHE   0.013   0.001   PHE E 369 
 TRP   0.011   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6737)
  covalent geometry    : angle       0.52833 ( 9153)
  SS BOND              : bond        0.00355 (    6)
  SS BOND              : angle       1.38930 (   12)
  hydrogen bonds       : bond        0.03509 (  322)
  hydrogen bonds       : angle       4.24052 (  915)
  link_NAG-ASN         : bond        0.00240 (    7)
  link_NAG-ASN         : angle       1.72137 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1245.56 seconds
wall clock time: 22 minutes 11.15 seconds (1331.15 seconds total)