Starting phenix.real_space_refine
on Tue Aug  4 16:42:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yx8_73599/08_2026/9yx8_73599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yx8_73599/08_2026/9yx8_73599.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yx8_73599/08_2026/9yx8_73599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yx8_73599/08_2026/9yx8_73599.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yx8_73599/08_2026/9yx8_73599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yx8_73599/08_2026/9yx8_73599.cif"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.013
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      17      5.16       5
     C    3148      2.51       5
     N     786      2.21       5
     O     897      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4848
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1537
          Classifications: {'peptide': 188}
          Link IDs: {'PTRANS': 11, 'TRANS': 176}
    Chain: "B"
      Number of atoms: 1690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1690
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 10, 'TRANS': 198}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 1537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1537
          Classifications: {'peptide': 188}
          Link IDs: {'PTRANS': 11, 'TRANS': 176}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.24, per 1000 atoms: 0.26
  Number of scatterers: 4848
  At special positions: 0
  Unit cell: (128.128, 84.032, 80.704, 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      17     16.00
     O     897      8.00
     N     786      7.00
     C    3148      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 331 "
      " NAG B1301 " - " ASN B 282 "
      " NAG B1302 " - " ASN B  61 "
      " NAG B1303 " - " ASN B 234 "
      " NAG C1301 " - " ASN C 343 "
      " NAG C1302 " - " ASN C 331 "
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 102.2 milliseconds
  

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1104

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 8 sheets defined
      13.5% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 4.371A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.651A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 4.042A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 390
      removed outlier: 4.517A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU C 390 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 410
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 439 through 441
      No H-bonds generated for 'chain 'C' and resid 439 through 441'
    Processing helix  chain 'C' and resid 445 through 449
      removed outlier: 3.591A  pdb=" N   TYR C 449 " --> pdb=" O   ASP C 446 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.156A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.652A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 30
      removed outlier: 8.037A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 5.514A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   PHE B 201 " --> pdb=" O   ASP B 228 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASP B 228 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ILE B 203 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 55
      removed outlier: 3.788A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 85
      removed outlier: 6.951A  pdb=" N   ARG B 237 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   PHE B 106 " --> pdb=" O   ARG B 237 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   GLN B 239 " --> pdb=" O   TRP B 104 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   TRP B 104 " --> pdb=" O   GLN B 239 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU B 241 " --> pdb=" O   ARG B 102 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   CYS B 131 " --> pdb=" O   SER B 116 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ILE B 128 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLU B 169 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   VAL B 130 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   GLU B 132 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ASN B 165 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358
    Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454

    143 hydrogen bonds defined for protein.
    336 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.68

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1487
        1.34 -     1.46: 1370
        1.46 -     1.58: 2118
        1.58 -     1.70: 0
        1.70 -     1.82: 17
  Bond restraints: 4992
  Sorted by residual:
  bond pdb=" N   ILE B 233 "
       pdb=" CA  ILE B 233 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.19e-02 7.06e+03 9.32e+00
  bond pdb=" N   GLU A 406 "
       pdb=" CA  GLU A 406 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.035 1.35e-02 5.49e+03 6.68e+00
  bond pdb=" N   ARG A 454 "
       pdb=" CA  ARG A 454 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.25e-02 6.40e+03 6.09e+00
  bond pdb=" N   TYR B 170 "
       pdb=" CA  TYR B 170 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.029 1.20e-02 6.94e+03 6.00e+00
  bond pdb=" N   ASN B 234 "
       pdb=" CA  ASN B 234 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.24e-02 6.50e+03 5.68e+00
  ... (remaining 4987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 6576
        1.55 -     3.10: 175
        3.10 -     4.65: 34
        4.65 -     6.20: 3
        6.20 -     7.76: 3
  Bond angle restraints: 6791
  Sorted by residual:
  angle pdb=" N   GLY B 107 "
        pdb=" CA  GLY B 107 "
        pdb=" C   GLY B 107 "
      ideal   model   delta    sigma   weight residual
     110.38  115.33   -4.95 1.28e+00 6.10e-01 1.50e+01
  angle pdb=" CA  LYS B 164 "
        pdb=" CB  LYS B 164 "
        pdb=" CG  LYS B 164 "
      ideal   model   delta    sigma   weight residual
     114.10  121.53   -7.43 2.00e+00 2.50e-01 1.38e+01
  angle pdb=" C   THR B 167 "
        pdb=" N   PHE B 168 "
        pdb=" CA  PHE B 168 "
      ideal   model   delta    sigma   weight residual
     122.94  119.01    3.93 1.50e+00 4.44e-01 6.87e+00
  angle pdb=" N   GLU A 406 "
        pdb=" CA  GLU A 406 "
        pdb=" C   GLU A 406 "
      ideal   model   delta    sigma   weight residual
     113.38  110.18    3.20 1.23e+00 6.61e-01 6.75e+00
  angle pdb=" CB  GLU A 340 "
        pdb=" CG  GLU A 340 "
        pdb=" CD  GLU A 340 "
      ideal   model   delta    sigma   weight residual
     112.60  117.01   -4.41 1.70e+00 3.46e-01 6.72e+00
  ... (remaining 6786 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 2642
       16.62 -    33.24: 261
       33.24 -    49.85: 63
       49.85 -    66.47: 17
       66.47 -    83.09: 3
  Dihedral angle restraints: 2986
    sinusoidal: 1259
      harmonic: 1727
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.09  -83.09     1      1.00e+01 1.00e-02 8.45e+01
  dihedral pdb=" CA  ASP B 111 "
           pdb=" C   ASP B 111 "
           pdb=" N   SER B 112 "
           pdb=" CA  SER B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.26  -17.74     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  CYS C 336 "
           pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -15.30  -57.70     1      2.00e+01 2.50e-03 1.12e+01
  ... (remaining 2983 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 563
       0.051 -    0.102: 124
       0.102 -    0.153: 42
       0.153 -    0.204: 3
       0.204 -    0.255: 1
  Chirality restraints: 733
  Sorted by residual:
  chirality pdb=" C1  NAG B1303 "
            pdb=" ND2 ASN B 234 "
            pdb=" C2  NAG B1303 "
            pdb=" O5  NAG B1303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CA  ARG B  34 "
            pdb=" N   ARG B  34 "
            pdb=" C   ARG B  34 "
            pdb=" CB  ARG B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CA  ILE B 233 "
            pdb=" N   ILE B 233 "
            pdb=" C   ILE B 233 "
            pdb=" CB  ILE B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.30e-01
  ... (remaining 730 not shown)

  Planarity restraints: 873
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B1303 "   -0.055 2.00e-02 2.50e+03   4.54e-02 2.58e+01
        pdb=" C7  NAG B1303 "    0.013 2.00e-02 2.50e+03
        pdb=" C8  NAG B1303 "   -0.041 2.00e-02 2.50e+03
        pdb=" N2  NAG B1303 "    0.073 2.00e-02 2.50e+03
        pdb=" O7  NAG B1303 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 454 "    0.234 9.50e-02 1.11e+02   1.05e-01 6.72e+00
        pdb=" NE  ARG A 454 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 454 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 454 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 454 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 346 "    0.201 9.50e-02 1.11e+02   9.06e-02 6.35e+00
        pdb=" NE  ARG A 346 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 346 "    0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 346 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 346 "    0.001 2.00e-02 2.50e+03
  ... (remaining 870 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 660
        2.76 -     3.29: 4304
        3.29 -     3.83: 7701
        3.83 -     4.36: 9519
        4.36 -     4.90: 16394
  Nonbonded interactions: 38578
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 442 "
            pdb=" OH  TYR A 451 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OE2 GLU C 406 "
            pdb=" OH  TYR C 495 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OH  TYR C 369 "
            pdb=" O   PRO C 384 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OH  TYR B  37 "
            pdb=" O   LEU B  54 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OD2 ASP C 398 "
            pdb=" OH  TYR C 423 "
     model   vdw
     2.316 3.040
  ... (remaining 38573 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 330 through 1301)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.760
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.040
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
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      :  0.004   0.040   5005  Z= 0.188
  Angle     :  0.628   7.756   6823  Z= 0.344
  Chirality :  0.049   0.255    733
  Planarity :  0.007   0.105    867
  Dihedral  : 13.970  79.875   1861
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 19.47 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.34), residues: 571
  helix: -2.90 (0.53), residues: 57
  sheet:  0.54 (0.42), residues: 164
  loop : -1.12 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 346 
 TYR   0.009   0.001   TYR C 495 
 PHE   0.019   0.001   PHE B 172 
 TRP   0.004   0.001   TRP A 436 
 HIS   0.001   0.000   HIS B  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.19 ( 4992)
  covalent geometry    : angle       0.62236 /  0.34 ( 6791)
  SS BOND              : bond        0.00240 /  0.13 (    7)
  SS BOND              : angle       1.43623 /  1.02 (   14)
  hydrogen bonds       : bond        0.22802 / 14.24 (  143)
  hydrogen bonds       : angle       9.25117 /  6.59 (  336)
  link_NAG-ASN         : bond        0.00220 /  0.15 (    6)
  link_NAG-ASN         : angle       1.30035 /  0.90 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8971 (m-30) cc_final: 0.8498 (m-30)
REVERT: A  450 ASN cc_start: 0.8098 (m-40) cc_final: 0.7598 (p0)
REVERT: A  465 GLU cc_start: 0.9132 (tt0) cc_final: 0.8791 (tt0)
REVERT: A  472 ILE cc_start: 0.8831 (mm) cc_final: 0.8103 (mp)
REVERT: B   41 LYS cc_start: 0.9074 (mmtm) cc_final: 0.7708 (mmtt)
REVERT: B  129 LYS cc_start: 0.8027 (mttt) cc_final: 0.7394 (mtpm)
REVERT: C  386 LYS cc_start: 0.8914 (mttm) cc_final: 0.7115 (ptmt)
REVERT: C  414 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8655 (mm-40)
REVERT: C  458 LYS cc_start: 0.9242 (mttt) cc_final: 0.8745 (mppt)
REVERT: C  462 LYS cc_start: 0.9060 (mttt) cc_final: 0.8854 (mtmm)
REVERT: C  465 GLU cc_start: 0.8926 (tt0) cc_final: 0.8382 (tt0)
REVERT: C  498 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8157 (mmm-85)
  outliers start: 4
  outliers final: 2
  residues processed: 102
  average time/residue: 0.6788
  time to fit residues: 71.5288
Evaluate side-chains
  90 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain C residue  489 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.1980
   chunk 50 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.088700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.066602 restraints weight = 10159.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 3.29
r_work: 0.2849 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5005  Z= 0.174
  Angle     :  0.549   6.249   6823  Z= 0.290
  Chirality :  0.047   0.157    733
  Planarity :  0.004   0.025    867
  Dihedral  :  5.888  55.453    779
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.85 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.34), residues: 571
  helix: -3.48 (0.55), residues: 40
  sheet:  0.37 (0.41), residues: 158
  loop : -0.99 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 346 
 TYR   0.010   0.001   TYR A 396 
 PHE   0.012   0.001   PHE B  65 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.001   0.000   HIS B 207 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.17 ( 4992)
  covalent geometry    : angle       0.54387 /  0.29 ( 6791)
  SS BOND              : bond        0.00170 /  0.10 (    7)
  SS BOND              : angle       1.22185 /  0.89 (   14)
  hydrogen bonds       : bond        0.04011 /  2.57 (  143)
  hydrogen bonds       : angle       6.94036 /  5.07 (  336)
  link_NAG-ASN         : bond        0.00194 /  0.11 (    6)
  link_NAG-ASN         : angle       1.20815 /  0.82 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8899 (m-30) cc_final: 0.8454 (m-30)
REVERT: A  450 ASN cc_start: 0.8078 (m-40) cc_final: 0.7525 (p0)
REVERT: A  465 GLU cc_start: 0.9155 (tt0) cc_final: 0.8781 (tt0)
REVERT: A  471 GLU cc_start: 0.7394 (pp20) cc_final: 0.7169 (pp20)
REVERT: B   41 LYS cc_start: 0.9069 (mmtm) cc_final: 0.7539 (tmtt)
REVERT: B  129 LYS cc_start: 0.7878 (mttt) cc_final: 0.7226 (mtpm)
REVERT: B  169 GLU cc_start: 0.8987 (tp30) cc_final: 0.8651 (tp30)
REVERT: B  212 VAL cc_start: 0.9144 (t) cc_final: 0.8889 (p)
REVERT: B  214 ARG cc_start: 0.8555 (ttm170) cc_final: 0.8080 (ttp-110)
REVERT: B  215 ASP cc_start: 0.8553 (t0) cc_final: 0.8240 (t0)
REVERT: C  386 LYS cc_start: 0.8969 (mttm) cc_final: 0.7349 (ptmt)
REVERT: C  414 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8837 (mm110)
REVERT: C  420 ASP cc_start: 0.8289 (m-30) cc_final: 0.7935 (m-30)
REVERT: C  458 LYS cc_start: 0.9230 (mttt) cc_final: 0.8763 (mppt)
REVERT: C  462 LYS cc_start: 0.9140 (mttt) cc_final: 0.8905 (mtpt)
REVERT: C  465 GLU cc_start: 0.9007 (tt0) cc_final: 0.8489 (tt0)
REVERT: C  474 GLN cc_start: 0.8694 (tp40) cc_final: 0.8304 (tp40)
REVERT: C  498 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8329 (mmm-85)
  outliers start: 18
  outliers final: 5
  residues processed: 105
  average time/residue: 0.6354
  time to fit residues: 68.8839
Evaluate side-chains
  93 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  489 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 52 optimal weight:    0.0980
   chunk 54 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0020
   chunk 11 optimal weight:    0.0170
   chunk 30 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.3426

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.090653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.068225 restraints weight = 10131.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 3.32
r_work: 0.2888 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5005  Z= 0.110
  Angle     :  0.512   5.227   6823  Z= 0.270
  Chirality :  0.046   0.152    733
  Planarity :  0.003   0.030    867
  Dihedral  :  5.680  56.256    777
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.99 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.34), residues: 571
  helix: -3.52 (0.52), residues: 40
  sheet:  0.42 (0.41), residues: 158
  loop : -0.95 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 346 
 TYR   0.007   0.001   TYR A 505 
 PHE   0.011   0.001   PHE B  65 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.000   HIS B  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 ( 4992)
  covalent geometry    : angle       0.50707 /  0.27 ( 6791)
  SS BOND              : bond        0.00083 /  0.05 (    7)
  SS BOND              : angle       1.05409 /  0.74 (   14)
  hydrogen bonds       : bond        0.03387 /  2.20 (  143)
  hydrogen bonds       : angle       6.49259 /  4.76 (  336)
  link_NAG-ASN         : bond        0.00235 /  0.15 (    6)
  link_NAG-ASN         : angle       1.15053 /  0.79 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8860 (m-30) cc_final: 0.8479 (m-30)
REVERT: A  450 ASN cc_start: 0.8034 (m-40) cc_final: 0.7526 (p0)
REVERT: A  465 GLU cc_start: 0.9157 (tt0) cc_final: 0.8828 (tt0)
REVERT: A  471 GLU cc_start: 0.7542 (pp20) cc_final: 0.7065 (pp20)
REVERT: B   41 LYS cc_start: 0.9048 (mmtm) cc_final: 0.7703 (mmtt)
REVERT: B  102 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7345 (tpp80)
REVERT: B  129 LYS cc_start: 0.7831 (mttt) cc_final: 0.7154 (mtpm)
REVERT: B  132 GLU cc_start: 0.7504 (mp0) cc_final: 0.7284 (mp0)
REVERT: B  169 GLU cc_start: 0.8979 (tp30) cc_final: 0.8623 (tp30)
REVERT: B  212 VAL cc_start: 0.9122 (t) cc_final: 0.8867 (p)
REVERT: B  214 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8097 (ttp-110)
REVERT: B  215 ASP cc_start: 0.8539 (t0) cc_final: 0.8198 (t0)
REVERT: C  386 LYS cc_start: 0.8955 (mttm) cc_final: 0.7305 (ptmt)
REVERT: C  414 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8749 (mm110)
REVERT: C  420 ASP cc_start: 0.8280 (m-30) cc_final: 0.7902 (m-30)
REVERT: C  458 LYS cc_start: 0.9218 (mttt) cc_final: 0.8766 (mppt)
REVERT: C  462 LYS cc_start: 0.9142 (mttt) cc_final: 0.8897 (mtpt)
REVERT: C  465 GLU cc_start: 0.8995 (tt0) cc_final: 0.8507 (tt0)
REVERT: C  474 GLN cc_start: 0.8714 (tp40) cc_final: 0.8403 (tp40)
REVERT: C  498 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8332 (mmm-85)
  outliers start: 16
  outliers final: 6
  residues processed: 107
  average time/residue: 0.6566
  time to fit residues: 72.4995
Evaluate side-chains
  95 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0370
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 493 GLN
B 185 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.090772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.068292 restraints weight = 10019.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 3.33
r_work: 0.2886 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5005  Z= 0.116
  Angle     :  0.502   5.100   6823  Z= 0.264
  Chirality :  0.046   0.155    733
  Planarity :  0.003   0.030    867
  Dihedral  :  5.538  55.627    777
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.99 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.34), residues: 571
  helix: -3.44 (0.54), residues: 40
  sheet:  0.44 (0.40), residues: 158
  loop : -0.92 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 346 
 TYR   0.007   0.001   TYR A 505 
 PHE   0.010   0.001   PHE C 486 
 TRP   0.005   0.001   TRP B  64 
 HIS   0.001   0.000   HIS B  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 4992)
  covalent geometry    : angle       0.49744 /  0.26 ( 6791)
  SS BOND              : bond        0.00169 /  0.10 (    7)
  SS BOND              : angle       1.06050 /  0.73 (   14)
  hydrogen bonds       : bond        0.03153 /  2.03 (  143)
  hydrogen bonds       : angle       6.23096 /  4.57 (  336)
  link_NAG-ASN         : bond        0.00215 /  0.14 (    6)
  link_NAG-ASN         : angle       1.12983 /  0.77 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8858 (m-30) cc_final: 0.8473 (m-30)
REVERT: A  450 ASN cc_start: 0.8023 (m-40) cc_final: 0.7533 (p0)
REVERT: A  455 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8131 (tt)
REVERT: A  465 GLU cc_start: 0.9149 (tt0) cc_final: 0.8833 (tt0)
REVERT: A  471 GLU cc_start: 0.7592 (pp20) cc_final: 0.7132 (pp20)
REVERT: B  129 LYS cc_start: 0.7857 (mttt) cc_final: 0.7168 (mtpm)
REVERT: B  132 GLU cc_start: 0.7465 (mp0) cc_final: 0.7149 (mp0)
REVERT: B  169 GLU cc_start: 0.8988 (tp30) cc_final: 0.8617 (tp30)
REVERT: B  212 VAL cc_start: 0.9121 (t) cc_final: 0.8839 (p)
REVERT: B  214 ARG cc_start: 0.8493 (ttm170) cc_final: 0.8151 (ttm110)
REVERT: B  215 ASP cc_start: 0.8551 (t0) cc_final: 0.8237 (t0)
REVERT: C  414 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8723 (mm110)
REVERT: C  420 ASP cc_start: 0.8288 (m-30) cc_final: 0.7892 (m-30)
REVERT: C  458 LYS cc_start: 0.9212 (mttt) cc_final: 0.8770 (mppt)
REVERT: C  462 LYS cc_start: 0.9140 (mttt) cc_final: 0.8900 (mtpt)
REVERT: C  465 GLU cc_start: 0.8995 (tt0) cc_final: 0.8512 (tt0)
REVERT: C  474 GLN cc_start: 0.8749 (tp40) cc_final: 0.8489 (tp-100)
REVERT: C  480 CYS cc_start: 0.5247 (p) cc_final: 0.4998 (p)
REVERT: C  498 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8362 (mmm-85)
  outliers start: 18
  outliers final: 9
  residues processed: 107
  average time/residue: 0.6219
  time to fit residues: 68.9233
Evaluate side-chains
  98 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  440 ARG
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0670
   overall best weight:    0.7118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 493 GLN
B 185 ASN
B 218 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.090373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.067956 restraints weight = 10212.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 3.35
r_work: 0.2876 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5005  Z= 0.133
  Angle     :  0.520   4.877   6823  Z= 0.273
  Chirality :  0.046   0.154    733
  Planarity :  0.003   0.036    867
  Dihedral  :  5.503  55.314    777
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.76 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.34), residues: 571
  helix: -3.43 (0.54), residues: 40
  sheet:  0.44 (0.40), residues: 158
  loop : -0.93 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 346 
 TYR   0.008   0.001   TYR A 505 
 PHE   0.009   0.001   PHE B  65 
 TRP   0.005   0.001   TRP B  64 
 HIS   0.001   0.000   HIS B  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 ( 4992)
  covalent geometry    : angle       0.51548 /  0.27 ( 6791)
  SS BOND              : bond        0.00225 /  0.13 (    7)
  SS BOND              : angle       1.11447 /  0.75 (   14)
  hydrogen bonds       : bond        0.03175 /  2.04 (  143)
  hydrogen bonds       : angle       6.16672 /  4.52 (  336)
  link_NAG-ASN         : bond        0.00200 /  0.13 (    6)
  link_NAG-ASN         : angle       1.11301 /  0.76 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.8697 (tt0) cc_final: 0.8267 (tt0)
REVERT: A  420 ASP cc_start: 0.8855 (m-30) cc_final: 0.8468 (m-30)
REVERT: A  455 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8162 (tt)
REVERT: A  465 GLU cc_start: 0.9148 (tt0) cc_final: 0.8831 (tt0)
REVERT: A  471 GLU cc_start: 0.7630 (pp20) cc_final: 0.7146 (pp20)
REVERT: B   41 LYS cc_start: 0.9042 (mmtm) cc_final: 0.7714 (mmtt)
REVERT: B  129 LYS cc_start: 0.7864 (mttt) cc_final: 0.7151 (mtpm)
REVERT: B  132 GLU cc_start: 0.7404 (mp0) cc_final: 0.7143 (mp0)
REVERT: B  169 GLU cc_start: 0.8974 (tp30) cc_final: 0.8566 (tp30)
REVERT: B  212 VAL cc_start: 0.9156 (t) cc_final: 0.8877 (p)
REVERT: B  215 ASP cc_start: 0.8512 (t0) cc_final: 0.8231 (t0)
REVERT: C  414 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8751 (mm110)
REVERT: C  420 ASP cc_start: 0.8312 (m-30) cc_final: 0.7910 (m-30)
REVERT: C  458 LYS cc_start: 0.9222 (mttt) cc_final: 0.8771 (mppt)
REVERT: C  462 LYS cc_start: 0.9143 (mttt) cc_final: 0.8900 (mtpt)
REVERT: C  465 GLU cc_start: 0.9001 (tt0) cc_final: 0.8511 (tt0)
REVERT: C  474 GLN cc_start: 0.8757 (tp40) cc_final: 0.8473 (tp40)
REVERT: C  480 CYS cc_start: 0.5110 (p) cc_final: 0.4803 (p)
REVERT: C  498 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8355 (mmm-85)
  outliers start: 16
  outliers final: 10
  residues processed: 108
  average time/residue: 0.6163
  time to fit residues: 68.8345
Evaluate side-chains
  98 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  440 ARG
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0770
   chunk 38 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    1.1342

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.088955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.066360 restraints weight = 10229.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 3.36
r_work: 0.2847 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8737
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5005  Z= 0.175
  Angle     :  0.543   5.228   6823  Z= 0.286
  Chirality :  0.047   0.156    733
  Planarity :  0.004   0.046    867
  Dihedral  :  5.565  54.897    777
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.76 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.34), residues: 571
  helix: -3.52 (0.54), residues: 40
  sheet:  0.35 (0.41), residues: 158
  loop : -0.93 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 346 
 TYR   0.009   0.001   TYR C 453 
 PHE   0.010   0.001   PHE C 486 
 TRP   0.007   0.001   TRP B  64 
 HIS   0.001   0.000   HIS B  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.18 ( 4992)
  covalent geometry    : angle       0.53857 /  0.29 ( 6791)
  SS BOND              : bond        0.00238 /  0.14 (    7)
  SS BOND              : angle       1.21001 /  0.82 (   14)
  hydrogen bonds       : bond        0.03370 /  2.13 (  143)
  hydrogen bonds       : angle       6.20869 /  4.54 (  336)
  link_NAG-ASN         : bond        0.00174 /  0.11 (    6)
  link_NAG-ASN         : angle       1.13885 /  0.77 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8845 (m-30) cc_final: 0.8425 (m-30)
REVERT: A  450 ASN cc_start: 0.8047 (m-40) cc_final: 0.7490 (p0)
REVERT: A  455 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8156 (tt)
REVERT: A  465 GLU cc_start: 0.9155 (tt0) cc_final: 0.8834 (tt0)
REVERT: A  471 GLU cc_start: 0.7656 (pp20) cc_final: 0.7158 (pp20)
REVERT: B   41 LYS cc_start: 0.9067 (mmtm) cc_final: 0.7578 (tmtt)
REVERT: B  129 LYS cc_start: 0.7866 (mttt) cc_final: 0.7111 (mtpm)
REVERT: B  132 GLU cc_start: 0.7461 (mp0) cc_final: 0.7099 (mp0)
REVERT: B  169 GLU cc_start: 0.8966 (tp30) cc_final: 0.8555 (tp30)
REVERT: B  187 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8363 (t)
REVERT: B  212 VAL cc_start: 0.9164 (t) cc_final: 0.8924 (p)
REVERT: B  214 ARG cc_start: 0.8524 (ttm170) cc_final: 0.8181 (ttm110)
REVERT: B  215 ASP cc_start: 0.8532 (t0) cc_final: 0.8263 (t0)
REVERT: C  414 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8799 (mm110)
REVERT: C  420 ASP cc_start: 0.8347 (m-30) cc_final: 0.7932 (m-30)
REVERT: C  458 LYS cc_start: 0.9223 (mttt) cc_final: 0.8775 (mppt)
REVERT: C  462 LYS cc_start: 0.9143 (mttt) cc_final: 0.8902 (mtpt)
REVERT: C  465 GLU cc_start: 0.9003 (tt0) cc_final: 0.8493 (tt0)
REVERT: C  474 GLN cc_start: 0.8791 (tp40) cc_final: 0.8481 (tp40)
REVERT: C  480 CYS cc_start: 0.5059 (p) cc_final: 0.4785 (p)
REVERT: C  498 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8441 (mmm-85)
  outliers start: 18
  outliers final: 9
  residues processed: 104
  average time/residue: 0.6164
  time to fit residues: 66.3497
Evaluate side-chains
  99 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  440 ARG
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 14 optimal weight:    0.1980
   chunk 9 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 44 optimal weight:    0.8980
   chunk 22 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.089793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.067354 restraints weight = 10060.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 3.33
r_work: 0.2873 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5005  Z= 0.131
  Angle     :  0.531   5.201   6823  Z= 0.279
  Chirality :  0.046   0.156    733
  Planarity :  0.003   0.047    867
  Dihedral  :  5.491  55.433    777
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.95 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.34), residues: 571
  helix: -3.51 (0.53), residues: 39
  sheet:  0.33 (0.41), residues: 158
  loop : -0.91 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 346 
 TYR   0.008   0.001   TYR A 505 
 PHE   0.009   0.001   PHE B  65 
 TRP   0.006   0.001   TRP B  64 
 HIS   0.001   0.000   HIS B  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 ( 4992)
  covalent geometry    : angle       0.52705 /  0.28 ( 6791)
  SS BOND              : bond        0.00191 /  0.11 (    7)
  SS BOND              : angle       1.09079 /  0.74 (   14)
  hydrogen bonds       : bond        0.03144 /  1.99 (  143)
  hydrogen bonds       : angle       6.11180 /  4.47 (  336)
  link_NAG-ASN         : bond        0.00191 /  0.12 (    6)
  link_NAG-ASN         : angle       1.11957 /  0.76 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8865 (m-30) cc_final: 0.8475 (m-30)
REVERT: A  465 GLU cc_start: 0.9137 (tt0) cc_final: 0.8811 (tt0)
REVERT: A  471 GLU cc_start: 0.7600 (pp20) cc_final: 0.7106 (pp20)
REVERT: B   41 LYS cc_start: 0.9056 (mmtm) cc_final: 0.7560 (tmtt)
REVERT: B  129 LYS cc_start: 0.7844 (mttt) cc_final: 0.7081 (mtpm)
REVERT: B  132 GLU cc_start: 0.7410 (mp0) cc_final: 0.7035 (mp0)
REVERT: B  169 GLU cc_start: 0.8971 (tp30) cc_final: 0.8559 (tp30)
REVERT: B  212 VAL cc_start: 0.9166 (t) cc_final: 0.8944 (p)
REVERT: B  214 ARG cc_start: 0.8520 (ttm170) cc_final: 0.8259 (mtm-85)
REVERT: B  215 ASP cc_start: 0.8450 (t0) cc_final: 0.8201 (t0)
REVERT: C  414 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8773 (mm110)
REVERT: C  420 ASP cc_start: 0.8313 (m-30) cc_final: 0.7934 (m-30)
REVERT: C  458 LYS cc_start: 0.9224 (mttt) cc_final: 0.8768 (mppt)
REVERT: C  462 LYS cc_start: 0.9127 (mttt) cc_final: 0.8882 (mtpt)
REVERT: C  465 GLU cc_start: 0.9002 (tt0) cc_final: 0.8499 (tt0)
REVERT: C  474 GLN cc_start: 0.8761 (tp40) cc_final: 0.8483 (tp40)
REVERT: C  480 CYS cc_start: 0.5092 (p) cc_final: 0.4818 (p)
REVERT: C  498 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8349 (mmm-85)
  outliers start: 18
  outliers final: 9
  residues processed: 108
  average time/residue: 0.6212
  time to fit residues: 69.5684
Evaluate side-chains
  98 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  440 ARG
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0570
   chunk 2 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.090107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.067715 restraints weight = 10215.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 3.35
r_work: 0.2879 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5005  Z= 0.128
  Angle     :  0.539   5.036   6823  Z= 0.283
  Chirality :  0.046   0.157    733
  Planarity :  0.004   0.054    867
  Dihedral  :  5.449  55.034    777
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 23.66 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.34), residues: 571
  helix: -3.60 (0.53), residues: 39
  sheet:  0.35 (0.41), residues: 158
  loop : -0.87 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 346 
 TYR   0.008   0.001   TYR A 505 
 PHE   0.012   0.001   PHE C 486 
 TRP   0.006   0.001   TRP B  64 
 HIS   0.001   0.000   HIS B  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 4992)
  covalent geometry    : angle       0.53525 /  0.28 ( 6791)
  SS BOND              : bond        0.00258 /  0.16 (    7)
  SS BOND              : angle       1.10429 /  0.75 (   14)
  hydrogen bonds       : bond        0.03102 /  1.97 (  143)
  hydrogen bonds       : angle       6.09194 /  4.44 (  336)
  link_NAG-ASN         : bond        0.00196 /  0.13 (    6)
  link_NAG-ASN         : angle       1.10596 /  0.76 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8820 (m-30) cc_final: 0.8437 (m-30)
REVERT: A  465 GLU cc_start: 0.9140 (tt0) cc_final: 0.8830 (tt0)
REVERT: A  471 GLU cc_start: 0.7595 (pp20) cc_final: 0.7098 (pp20)
REVERT: B   41 LYS cc_start: 0.9052 (mmtm) cc_final: 0.7556 (tmtt)
REVERT: B  111 ASP cc_start: 0.8105 (p0) cc_final: 0.7665 (p0)
REVERT: B  129 LYS cc_start: 0.7843 (mttt) cc_final: 0.7081 (mtpm)
REVERT: B  132 GLU cc_start: 0.7390 (mp0) cc_final: 0.7122 (mp0)
REVERT: B  169 GLU cc_start: 0.8979 (tp30) cc_final: 0.8565 (tp30)
REVERT: B  214 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8243 (mtm-85)
REVERT: C  414 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8745 (mm110)
REVERT: C  420 ASP cc_start: 0.8355 (m-30) cc_final: 0.8001 (m-30)
REVERT: C  458 LYS cc_start: 0.9228 (mttt) cc_final: 0.8766 (mppt)
REVERT: C  462 LYS cc_start: 0.9126 (mttt) cc_final: 0.8878 (mtpt)
REVERT: C  465 GLU cc_start: 0.9012 (tt0) cc_final: 0.8513 (tt0)
REVERT: C  474 GLN cc_start: 0.8788 (tp40) cc_final: 0.8467 (tp40)
REVERT: C  480 CYS cc_start: 0.5030 (p) cc_final: 0.4791 (p)
REVERT: C  498 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8337 (mmm-85)
  outliers start: 13
  outliers final: 10
  residues processed: 99
  average time/residue: 0.6985
  time to fit residues: 71.4638
Evaluate side-chains
  99 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  440 ARG
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0770
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.5538

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.090437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.068116 restraints weight = 10070.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 3.33
r_work: 0.2889 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5005  Z= 0.126
  Angle     :  0.556   6.173   6823  Z= 0.290
  Chirality :  0.046   0.153    733
  Planarity :  0.004   0.056    867
  Dihedral  :  5.416  55.555    777
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 24.05 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.34), residues: 571
  helix: -3.59 (0.52), residues: 39
  sheet:  0.33 (0.41), residues: 151
  loop : -0.93 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 346 
 TYR   0.007   0.001   TYR A 505 
 PHE   0.009   0.001   PHE B  65 
 TRP   0.005   0.001   TRP B  64 
 HIS   0.001   0.000   HIS B  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 4992)
  covalent geometry    : angle       0.55196 /  0.29 ( 6791)
  SS BOND              : bond        0.00245 /  0.13 (    7)
  SS BOND              : angle       1.15525 /  0.77 (   14)
  hydrogen bonds       : bond        0.03041 /  1.93 (  143)
  hydrogen bonds       : angle       6.02932 /  4.39 (  336)
  link_NAG-ASN         : bond        0.00206 /  0.13 (    6)
  link_NAG-ASN         : angle       1.11674 /  0.77 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8803 (m-30) cc_final: 0.8423 (m-30)
REVERT: A  465 GLU cc_start: 0.9127 (tt0) cc_final: 0.8838 (tt0)
REVERT: A  471 GLU cc_start: 0.7597 (pp20) cc_final: 0.7098 (pp20)
REVERT: B   41 LYS cc_start: 0.9055 (mmtm) cc_final: 0.7575 (tmtt)
REVERT: B  129 LYS cc_start: 0.7863 (mttt) cc_final: 0.7103 (mtpm)
REVERT: B  132 GLU cc_start: 0.7382 (mp0) cc_final: 0.7140 (mp0)
REVERT: B  169 GLU cc_start: 0.8964 (tp30) cc_final: 0.8583 (tp30)
REVERT: B  214 ARG cc_start: 0.8494 (ttm170) cc_final: 0.8226 (mtm-85)
REVERT: C  414 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8703 (mm110)
REVERT: C  420 ASP cc_start: 0.8364 (m-30) cc_final: 0.8014 (m-30)
REVERT: C  458 LYS cc_start: 0.9220 (mttt) cc_final: 0.8760 (mppt)
REVERT: C  462 LYS cc_start: 0.9128 (mttt) cc_final: 0.8886 (mtpt)
REVERT: C  465 GLU cc_start: 0.9013 (tt0) cc_final: 0.8528 (tt0)
REVERT: C  474 GLN cc_start: 0.8786 (tp40) cc_final: 0.8553 (tp40)
REVERT: C  498 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8343 (mmm-85)
  outliers start: 13
  outliers final: 9
  residues processed: 102
  average time/residue: 0.6040
  time to fit residues: 63.5951
Evaluate side-chains
  96 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  185 ASN
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  440 ARG
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 45 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.089822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.067487 restraints weight = 10165.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 3.33
r_work: 0.2874 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8731
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5005  Z= 0.142
  Angle     :  0.575   6.627   6823  Z= 0.300
  Chirality :  0.047   0.151    733
  Planarity :  0.004   0.060    867
  Dihedral  :  5.444  55.159    777
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 24.62 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.34), residues: 571
  helix: -3.60 (0.51), residues: 39
  sheet:  0.37 (0.39), residues: 170
  loop : -0.87 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 346 
 TYR   0.008   0.001   TYR A 505 
 PHE   0.015   0.001   PHE C 486 
 TRP   0.006   0.001   TRP B  64 
 HIS   0.001   0.000   HIS B  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.14 ( 4992)
  covalent geometry    : angle       0.56954 /  0.30 ( 6791)
  SS BOND              : bond        0.00182 /  0.10 (    7)
  SS BOND              : angle       1.41215 /  1.07 (   14)
  hydrogen bonds       : bond        0.03135 /  1.98 (  143)
  hydrogen bonds       : angle       6.06810 /  4.41 (  336)
  link_NAG-ASN         : bond        0.00175 /  0.11 (    6)
  link_NAG-ASN         : angle       1.11649 /  0.77 (   18)

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

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

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1142 Ramachandran restraints generated.
    571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8816 (m-30) cc_final: 0.8432 (m-30)
REVERT: A  450 ASN cc_start: 0.8043 (m-40) cc_final: 0.7549 (p0)
REVERT: A  465 GLU cc_start: 0.9123 (tt0) cc_final: 0.8849 (tt0)
REVERT: A  471 GLU cc_start: 0.7588 (pp20) cc_final: 0.7085 (pp20)
REVERT: B   41 LYS cc_start: 0.9068 (mmtm) cc_final: 0.7596 (tmtt)
REVERT: B  129 LYS cc_start: 0.7890 (mttt) cc_final: 0.7160 (mtpm)
REVERT: B  132 GLU cc_start: 0.7421 (mp0) cc_final: 0.7191 (mp0)
REVERT: B  169 GLU cc_start: 0.8935 (tp30) cc_final: 0.8630 (tp30)
REVERT: C  414 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8717 (mm110)
REVERT: C  420 ASP cc_start: 0.8404 (m-30) cc_final: 0.8058 (m-30)
REVERT: C  458 LYS cc_start: 0.9210 (mttt) cc_final: 0.8767 (mppt)
REVERT: C  462 LYS cc_start: 0.9143 (mttt) cc_final: 0.8910 (mtpt)
REVERT: C  465 GLU cc_start: 0.9018 (tt0) cc_final: 0.8542 (tt0)
REVERT: C  474 GLN cc_start: 0.8814 (tp40) cc_final: 0.8490 (tp40)
REVERT: C  498 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8456 (mmm-85)
  outliers start: 11
  outliers final: 9
  residues processed: 96
  average time/residue: 0.6005
  time to fit residues: 59.6265
Evaluate side-chains
  96 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  440 ARG
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 52 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0070
   overall best weight:    0.4598

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.090834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.068592 restraints weight = 10144.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 3.35
r_work: 0.2898 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8713
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5005  Z= 0.120
  Angle     :  0.564   6.494   6823  Z= 0.294
  Chirality :  0.046   0.152    733
  Planarity :  0.004   0.059    867
  Dihedral  :  5.398  55.528    777
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 24.62 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.34), residues: 571
  helix: -3.56 (0.52), residues: 39
  sheet:  0.41 (0.39), residues: 163
  loop : -0.94 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 346 
 TYR   0.007   0.001   TYR A 505 
 PHE   0.009   0.001   PHE B  65 
 TRP   0.005   0.001   TRP B  64 
 HIS   0.001   0.000   HIS B  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 4992)
  covalent geometry    : angle       0.55931 /  0.29 ( 6791)
  SS BOND              : bond        0.00193 /  0.11 (    7)
  SS BOND              : angle       1.24776 /  0.91 (   14)
  hydrogen bonds       : bond        0.02974 /  1.89 (  143)
  hydrogen bonds       : angle       5.98023 /  4.34 (  336)
  link_NAG-ASN         : bond        0.00198 /  0.13 (    6)
  link_NAG-ASN         : angle       1.12898 /  0.78 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2192.44 seconds
wall clock time: 38 minutes 4.18 seconds (2284.18 seconds total)