Starting phenix.real_space_refine
on Tue Aug  4 13:31:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v3v_64757/08_2026/9v3v_64757_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v3v_64757/08_2026/9v3v_64757.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v3v_64757/08_2026/9v3v_64757.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v3v_64757/08_2026/9v3v_64757.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v3v_64757/08_2026/9v3v_64757_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v3v_64757/08_2026/9v3v_64757_trim.cif"
  }
  resolution = 3.37
  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=  -0.002 sd=   0.065
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      23      5.16       5
     C    2224      2.51       5
     N     529      2.21       5
     O     571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  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: 3347
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 424, 3326
          Classifications: {'peptide': 424}
          Link IDs: {'PTRANS': 22, 'TRANS': 401}
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 21
          Unusual residues: {'4AX': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.11, per 1000 atoms: 0.33
  Number of scatterers: 3347
  At special positions: 0
  Unit cell: (75.53, 68.89, 73.04, 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      23     16.00
     O     571      8.00
     N     529      7.00
     C    2224      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 180 " - pdb=" SG  CYS A 329 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 501 " - " ASN A 174 "
  Time building additional restraints: 0.30
  Conformation dependent library (CDL) restraints added in 134.2 milliseconds
  

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      77.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 59
      removed outlier: 3.546A  pdb=" N   GLY A  59 " --> pdb=" O   HIS A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 67 through 76
    Processing helix  chain 'A' and resid 78 through 109
      removed outlier: 3.692A  pdb=" N   ILE A  82 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   MET A  95 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU A  98 " --> pdb=" O   CYS A  94 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE A 105 " --> pdb=" O   CYS A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 126
      removed outlier: 3.956A  pdb=" N   VAL A 120 " --> pdb=" O   TYR A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 137
      removed outlier: 4.083A  pdb=" N   ARG A 133 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASN A 134 " --> pdb=" O   TRP A 131 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   HIS A 137 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 172
      removed outlier: 3.733A  pdb=" N   ILE A 148 " --> pdb=" O   ASP A 144 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 152 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   CYS A 155 " --> pdb=" O   GLN A 151 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   TYR A 158 " --> pdb=" O   PHE A 154 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 162 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LYS A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 3.721A  pdb=" N   MET A 198 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU A 199 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
      Proline residue:  A 203  - end of helix
      removed outlier: 3.937A  pdb=" N   LEU A 207 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 240
      removed outlier: 3.641A  pdb=" N   ILE A 219 " --> pdb=" O   ARG A 215 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ASN A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ILE A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 240 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 266
      removed outlier: 3.941A  pdb=" N   THR A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 282
      removed outlier: 3.693A  pdb=" N   LYS A 281 " --> pdb=" O   PRO A 277 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   MET A 282 " --> pdb=" O   LEU A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 286
      No H-bonds generated for 'chain 'A' and resid 284 through 286'
    Processing helix  chain 'A' and resid 287 through 315
      removed outlier: 3.669A  pdb=" N   ILE A 291 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL A 299 " --> pdb=" O   GLY A 295 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   THR A 300 " --> pdb=" O   MET A 296 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   TYR A 311 " --> pdb=" O   GLY A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 321 through 325
    Processing helix  chain 'A' and resid 329 through 364
      removed outlier: 4.012A  pdb=" N   ALA A 348 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   VAL A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      Proline residue:  A 354  - end of helix
      Proline residue:  A 360  - end of helix
    Processing helix  chain 'A' and resid 371 through 379
      removed outlier: 3.957A  pdb=" N   ASP A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 392
      removed outlier: 3.519A  pdb=" N   LEU A 392 " --> pdb=" O   ILE A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 407
      removed outlier: 3.682A  pdb=" N   ILE A 400 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   SER A 401 " --> pdb=" O   ASP A 397 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   SER A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 412
      removed outlier: 3.508A  pdb=" N   LEU A 411 " --> pdb=" O   SER A 407 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ALA A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 407 through 412'
    Processing helix  chain 'A' and resid 414 through 423
    Processing helix  chain 'A' and resid 430 through 455
      removed outlier: 4.122A  pdb=" N   THR A 452 " --> pdb=" O   PHE A 448 " (cutoff:3.500A)

    195 hydrogen bonds defined for protein.
    573 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: 0.51

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 500
        1.31 -     1.43: 933
        1.43 -     1.56: 1964
        1.56 -     1.68: 2
        1.68 -     1.81: 34
  Bond restraints: 3433
  Sorted by residual:
  bond pdb=" CA  4AX A 502 "
       pdb=" C3  4AX A 502 "
    ideal  model  delta    sigma   weight residual
    1.525  1.375  0.150 2.00e-02 2.50e+03 5.61e+01
  bond pdb=" C3  4AX A 502 "
       pdb=" NXT 4AX A 502 "
    ideal  model  delta    sigma   weight residual
    1.345  1.478 -0.133 2.00e-02 2.50e+03 4.39e+01
  bond pdb=" O   4AX A 502 "
       pdb=" NXT 4AX A 502 "
    ideal  model  delta    sigma   weight residual
    1.386  1.279  0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" C   ILE A  61 "
       pdb=" O   ILE A  61 "
    ideal  model  delta    sigma   weight residual
    1.236  1.190  0.046 1.19e-02 7.06e+03 1.49e+01
  bond pdb=" CB  PRO A 246 "
       pdb=" CG  PRO A 246 "
    ideal  model  delta    sigma   weight residual
    1.492  1.674 -0.182 5.00e-02 4.00e+02 1.32e+01
  ... (remaining 3428 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 4652
        2.94 -     5.89: 27
        5.89 -     8.83: 3
        8.83 -    11.77: 0
       11.77 -    14.72: 1
  Bond angle restraints: 4683
  Sorted by residual:
  angle pdb=" CA  PRO A 246 "
        pdb=" N   PRO A 246 "
        pdb=" CD  PRO A 246 "
      ideal   model   delta    sigma   weight residual
     112.00   97.28   14.72 1.40e+00 5.10e-01 1.11e+02
  angle pdb=" N   PHE A 267 "
        pdb=" CA  PHE A 267 "
        pdb=" C   PHE A 267 "
      ideal   model   delta    sigma   weight residual
     113.18  105.87    7.31 1.33e+00 5.65e-01 3.02e+01
  angle pdb=" N   PRO A 246 "
        pdb=" CD  PRO A 246 "
        pdb=" CG  PRO A 246 "
      ideal   model   delta    sigma   weight residual
     103.20   96.55    6.65 1.50e+00 4.44e-01 1.97e+01
  angle pdb=" CA  PRO A 327 "
        pdb=" N   PRO A 327 "
        pdb=" CD  PRO A 327 "
      ideal   model   delta    sigma   weight residual
     112.00  106.26    5.74 1.40e+00 5.10e-01 1.68e+01
  angle pdb=" CA  PHE A 267 "
        pdb=" C   PHE A 267 "
        pdb=" N   SER A 268 "
      ideal   model   delta    sigma   weight residual
     118.22  115.06    3.16 1.03e+00 9.43e-01 9.44e+00
  ... (remaining 4678 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.33: 1871
       15.33 -    30.67: 118
       30.67 -    46.00: 28
       46.00 -    61.33: 7
       61.33 -    76.67: 3
  Dihedral angle restraints: 2027
    sinusoidal: 796
      harmonic: 1231
  Sorted by residual:
  dihedral pdb=" CA  ILE A 266 "
           pdb=" C   ILE A 266 "
           pdb=" N   PHE A 267 "
           pdb=" CA  PHE A 267 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.23   18.77     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  GLU A 270 "
           pdb=" C   GLU A 270 "
           pdb=" N   GLY A 271 "
           pdb=" CA  GLY A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.16   16.84     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CB  MET A  95 "
           pdb=" CG  MET A  95 "
           pdb=" SD  MET A  95 "
           pdb=" CE  MET A  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.35  -57.65     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 2024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 475
       0.053 -    0.107: 87
       0.107 -    0.160: 5
       0.160 -    0.213: 0
       0.213 -    0.267: 1
  Chirality restraints: 568
  Sorted by residual:
  chirality pdb=" CA  4AX A 502 "
            pdb=" N   4AX A 502 "
            pdb=" CB  4AX A 502 "
            pdb=" C3  4AX A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.82    2.55    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" C1  NAG A 501 "
            pdb=" ND2 ASN A 174 "
            pdb=" C2  NAG A 501 "
            pdb=" O5  NAG A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-01 2.50e+01 5.26e-01
  chirality pdb=" CA  ILE A 393 "
            pdb=" N   ILE A 393 "
            pdb=" C   ILE A 393 "
            pdb=" CB  ILE A 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.66e-01
  ... (remaining 565 not shown)

  Planarity restraints: 572
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 245 "    0.077 5.00e-02 4.00e+02   1.06e-01 1.79e+01
        pdb=" N   PRO A 246 "   -0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO A 246 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 246 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 326 "    0.066 5.00e-02 4.00e+02   9.77e-02 1.53e+01
        pdb=" N   PRO A 327 "   -0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO A 327 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 327 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  61 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.57e+00
        pdb=" C   ILE A  61 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ILE A  61 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLY A  62 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 569 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 50
        2.67 -     3.22: 3657
        3.22 -     3.78: 5035
        3.78 -     4.34: 7315
        4.34 -     4.90: 11697
  Nonbonded interactions: 27754
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 270 "
            pdb=" OG  SER A 408 "
     model   vdw
     2.107 3.040
  nonbonded pdb=" OE1 GLN A 168 "
            pdb=" NZ  LYS A 336 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" OG  SER A 426 "
            pdb=" OE1 GLU A 427 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OD1 ASN A 134 "
            pdb=" N   HIS A 135 "
     model   vdw
     2.363 3.120
  nonbonded pdb=" O3  NAG A 501 "
            pdb=" O7  NAG A 501 "
     model   vdw
     2.366 3.040
  ... (remaining 27749 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.710
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
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      :  0.006   0.182   3435  Z= 0.280
  Angle     :  0.672  14.717   4688  Z= 0.422
  Chirality :  0.041   0.267    568
  Planarity :  0.007   0.106    571
  Dihedral  : 11.806  76.668   1232
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 38.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  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: -1.36 (0.45), residues: 422
  helix: -0.80 (0.31), residues: 301
  sheet:  None (None), residues: 0
  loop : -0.70 (0.69), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 141 
 TYR   0.008   0.001   TYR A 116 
 PHE   0.006   0.001   PHE A 344 
 TRP   0.007   0.001   TRP A 330 
 HIS   0.002   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00627 /  0.28 ( 3433)
  covalent geometry    : angle       0.67163 /  0.42 ( 4683)
  SS BOND              : bond        0.00226 /  0.14 (    1)
  SS BOND              : angle       0.18679 /  0.06 (    2)
  hydrogen bonds       : bond        0.19776 / 12.57 (  195)
  hydrogen bonds       : angle       9.35773 /  6.52 (  573)
  link_NAG-ASN         : bond        0.00266 /  0.17 (    1)
  link_NAG-ASN         : angle       1.00844 /  0.37 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  121 MET cc_start: 0.7055 (ttt) cc_final: 0.6781 (ttp)
REVERT: A  256 LYS cc_start: 0.7406 (mmtm) cc_final: 0.7106 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0518
  time to fit residues: 4.1940
Evaluate side-chains
  55 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 325 ASN ** 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 = 0.4056 r_free = 0.4056 target = 0.167721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.138650 restraints weight = 3936.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 2.23
r_work: 0.3572 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   3435  Z= 0.169
  Angle     :  0.718   8.048   4688  Z= 0.351
  Chirality :  0.045   0.172    568
  Planarity :  0.006   0.058    571
  Dihedral  :  5.796  40.671    481
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  7.22 %
    Favored  : 91.18 %
  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: -1.40 (0.43), residues: 422
  helix: -0.81 (0.29), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.72 (0.76), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 365 
 TYR   0.016   0.002   TYR A 116 
 PHE   0.015   0.002   PHE A 262 
 TRP   0.004   0.001   TRP A 138 
 HIS   0.003   0.001   HIS A 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.17 ( 3433)
  covalent geometry    : angle       0.71747 /  0.35 ( 4683)
  SS BOND              : bond        0.00031 /  0.02 (    1)
  SS BOND              : angle       0.47518 /  0.22 (    2)
  hydrogen bonds       : bond        0.04120 /  2.63 (  195)
  hydrogen bonds       : angle       5.12356 /  3.59 (  573)
  link_NAG-ASN         : bond        0.00372 /  0.23 (    1)
  link_NAG-ASN         : angle       1.15540 /  0.47 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  121 MET cc_start: 0.7116 (ttt) cc_final: 0.6710 (ttp)
REVERT: A  179 ASN cc_start: 0.8116 (t0) cc_final: 0.7847 (t0)
REVERT: A  256 LYS cc_start: 0.7243 (mmtm) cc_final: 0.6673 (pttp)
  outliers start: 6
  outliers final: 2
  residues processed: 63
  average time/residue: 0.0471
  time to fit residues: 4.0115
Evaluate side-chains
  54 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  189 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.2980
   chunk 10 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0980
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.171520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.141409 restraints weight = 3900.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.32
r_work: 0.3593 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3435  Z= 0.140
  Angle     :  0.649   8.281   4688  Z= 0.316
  Chirality :  0.043   0.178    568
  Planarity :  0.006   0.054    571
  Dihedral  :  5.274  37.869    481
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  :  7.49 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.43), residues: 422
  helix: -0.46 (0.29), residues: 316
  sheet:  None (None), residues: 0
  loop : -0.64 (0.74), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.012   0.001   TYR A 116 
 PHE   0.016   0.001   PHE A 448 
 TRP   0.004   0.001   TRP A  49 
 HIS   0.002   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.14 ( 3433)
  covalent geometry    : angle       0.64813 /  0.32 ( 4683)
  SS BOND              : bond        0.00307 /  0.19 (    1)
  SS BOND              : angle       1.02732 /  0.38 (    2)
  hydrogen bonds       : bond        0.03545 /  2.28 (  195)
  hydrogen bonds       : angle       4.55694 /  3.19 (  573)
  link_NAG-ASN         : bond        0.00326 /  0.20 (    1)
  link_NAG-ASN         : angle       1.08367 /  0.42 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  121 MET cc_start: 0.7099 (ttt) cc_final: 0.6672 (ttp)
REVERT: A  179 ASN cc_start: 0.8254 (t0) cc_final: 0.7860 (t0)
REVERT: A  256 LYS cc_start: 0.7351 (mmtm) cc_final: 0.6767 (pttp)
  outliers start: 13
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0482
  time to fit residues: 4.1590
Evaluate side-chains
  61 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  439 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 14 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.167395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.138271 restraints weight = 3858.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.22
r_work: 0.3577 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3435  Z= 0.149
  Angle     :  0.632   7.876   4688  Z= 0.308
  Chirality :  0.044   0.322    568
  Planarity :  0.006   0.055    571
  Dihedral  :  5.091  36.263    481
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.43 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.43), residues: 422
  helix: -0.28 (0.29), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.69 (0.74), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 395 
 TYR   0.013   0.001   TYR A 116 
 PHE   0.015   0.001   PHE A 448 
 TRP   0.004   0.001   TRP A 330 
 HIS   0.003   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.15 ( 3433)
  covalent geometry    : angle       0.63103 /  0.31 ( 4683)
  SS BOND              : bond        0.00297 /  0.19 (    1)
  SS BOND              : angle       0.89905 /  0.33 (    2)
  hydrogen bonds       : bond        0.03414 /  2.18 (  195)
  hydrogen bonds       : angle       4.33096 /  3.04 (  573)
  link_NAG-ASN         : bond        0.00243 /  0.15 (    1)
  link_NAG-ASN         : angle       1.07028 /  0.41 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8762 (ptpp) cc_final: 0.8272 (ptpp)
REVERT: A  121 MET cc_start: 0.7041 (ttt) cc_final: 0.6598 (ttp)
REVERT: A  179 ASN cc_start: 0.8254 (t0) cc_final: 0.7861 (t0)
REVERT: A  237 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7974 (tt0)
REVERT: A  256 LYS cc_start: 0.7344 (mmtm) cc_final: 0.6753 (pttp)
  outliers start: 9
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0506
  time to fit residues: 4.0177
Evaluate side-chains
  57 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  397 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.0770
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 168 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 = 0.4054 r_free = 0.4054 target = 0.167498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.138097 restraints weight = 3835.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.21
r_work: 0.3580 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3435  Z= 0.143
  Angle     :  0.624   7.901   4688  Z= 0.304
  Chirality :  0.043   0.245    568
  Planarity :  0.006   0.055    571
  Dihedral  :  5.012  34.251    481
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 11.76 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.43), residues: 422
  helix: -0.18 (0.29), residues: 315
  sheet:  None (None), residues: 0
  loop : -0.59 (0.74), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 395 
 TYR   0.011   0.001   TYR A 116 
 PHE   0.015   0.001   PHE A 448 
 TRP   0.004   0.001   TRP A 330 
 HIS   0.003   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.14 ( 3433)
  covalent geometry    : angle       0.62345 /  0.30 ( 4683)
  SS BOND              : bond        0.00229 /  0.14 (    1)
  SS BOND              : angle       0.71688 /  0.26 (    2)
  hydrogen bonds       : bond        0.03306 /  2.12 (  195)
  hydrogen bonds       : angle       4.26303 /  2.99 (  573)
  link_NAG-ASN         : bond        0.00221 /  0.14 (    1)
  link_NAG-ASN         : angle       1.10045 /  0.43 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8838 (ptpp) cc_final: 0.8341 (ptpp)
REVERT: A  179 ASN cc_start: 0.8245 (t0) cc_final: 0.7841 (t0)
REVERT: A  207 LEU cc_start: 0.7428 (mt) cc_final: 0.7106 (pp)
REVERT: A  232 LEU cc_start: 0.8659 (tp) cc_final: 0.8456 (tp)
REVERT: A  256 LYS cc_start: 0.7449 (mmtm) cc_final: 0.6861 (pttp)
  outliers start: 9
  outliers final: 7
  residues processed: 57
  average time/residue: 0.0530
  time to fit residues: 3.9669
Evaluate side-chains
  58 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  439 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    0.2980
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.168620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.139303 restraints weight = 3819.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.22
r_work: 0.3593 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3435  Z= 0.131
  Angle     :  0.605   7.863   4688  Z= 0.295
  Chirality :  0.042   0.202    568
  Planarity :  0.006   0.057    571
  Dihedral  :  4.880  31.913    481
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.57 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.43), residues: 422
  helix: -0.01 (0.29), residues: 315
  sheet:  None (None), residues: 0
  loop : -0.63 (0.74), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 195 
 TYR   0.008   0.001   TYR A 116 
 PHE   0.015   0.001   PHE A 448 
 TRP   0.004   0.001   TRP A 330 
 HIS   0.002   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.13 ( 3433)
  covalent geometry    : angle       0.60436 /  0.29 ( 4683)
  SS BOND              : bond        0.00205 /  0.13 (    1)
  SS BOND              : angle       0.62960 /  0.23 (    2)
  hydrogen bonds       : bond        0.03167 /  2.03 (  195)
  hydrogen bonds       : angle       4.14833 /  2.90 (  573)
  link_NAG-ASN         : bond        0.00219 /  0.14 (    1)
  link_NAG-ASN         : angle       1.07692 /  0.43 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8851 (ptpp) cc_final: 0.8376 (ptpp)
REVERT: A  121 MET cc_start: 0.7144 (ttt) cc_final: 0.6715 (ttp)
REVERT: A  179 ASN cc_start: 0.8281 (t0) cc_final: 0.7896 (t0)
REVERT: A  232 LEU cc_start: 0.8669 (tp) cc_final: 0.8436 (tp)
REVERT: A  256 LYS cc_start: 0.7511 (mmtm) cc_final: 0.6946 (pttp)
  outliers start: 9
  outliers final: 8
  residues processed: 57
  average time/residue: 0.0526
  time to fit residues: 3.9619
Evaluate side-chains
  60 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  439 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 36 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 168 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 = 0.4059 r_free = 0.4059 target = 0.168234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.138591 restraints weight = 3922.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 2.25
r_work: 0.3589 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3435  Z= 0.140
  Angle     :  0.608   7.930   4688  Z= 0.297
  Chirality :  0.042   0.184    568
  Planarity :  0.006   0.060    571
  Dihedral  :  4.839  30.160    481
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 13.10 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.28 (0.43), residues: 422
  helix:  0.09 (0.29), residues: 315
  sheet:  None (None), residues: 0
  loop : -0.63 (0.73), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 195 
 TYR   0.009   0.001   TYR A 116 
 PHE   0.027   0.001   PHE A 448 
 TRP   0.003   0.001   TRP A  49 
 HIS   0.003   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.14 ( 3433)
  covalent geometry    : angle       0.60754 /  0.30 ( 4683)
  SS BOND              : bond        0.00191 /  0.12 (    1)
  SS BOND              : angle       0.59969 /  0.22 (    2)
  hydrogen bonds       : bond        0.03161 /  2.03 (  195)
  hydrogen bonds       : angle       4.15662 /  2.91 (  573)
  link_NAG-ASN         : bond        0.00229 /  0.14 (    1)
  link_NAG-ASN         : angle       1.01607 /  0.40 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8368 (ptpp)
REVERT: A  121 MET cc_start: 0.7116 (ttt) cc_final: 0.6696 (ttp)
REVERT: A  179 ASN cc_start: 0.8303 (t0) cc_final: 0.7919 (t0)
REVERT: A  207 LEU cc_start: 0.7384 (mt) cc_final: 0.7084 (pp)
REVERT: A  232 LEU cc_start: 0.8727 (tp) cc_final: 0.8483 (tp)
REVERT: A  256 LYS cc_start: 0.7519 (mmtm) cc_final: 0.6955 (pttp)
  outliers start: 9
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0357
  time to fit residues: 2.7721
Evaluate side-chains
  61 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  439 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0010
   chunk 18 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 168 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 = 0.3861 r_free = 0.3861 target = 0.156235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.125840 restraints weight = 3847.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.35
r_work: 0.3396 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3435  Z= 0.136
  Angle     :  0.606   7.874   4688  Z= 0.296
  Chirality :  0.042   0.175    568
  Planarity :  0.006   0.061    571
  Dihedral  :  4.792  28.184    481
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 12.57 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.43), residues: 422
  helix:  0.12 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -0.54 (0.74), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 195 
 TYR   0.008   0.001   TYR A 116 
 PHE   0.024   0.001   PHE A 448 
 TRP   0.003   0.001   TRP A  49 
 HIS   0.002   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.14 ( 3433)
  covalent geometry    : angle       0.60529 /  0.30 ( 4683)
  SS BOND              : bond        0.00203 /  0.13 (    1)
  SS BOND              : angle       0.60771 /  0.22 (    2)
  hydrogen bonds       : bond        0.03138 /  2.00 (  195)
  hydrogen bonds       : angle       4.13291 /  2.89 (  573)
  link_NAG-ASN         : bond        0.00223 /  0.14 (    1)
  link_NAG-ASN         : angle       1.00385 /  0.40 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8677 (ptpp) cc_final: 0.8115 (ptpp)
REVERT: A  121 MET cc_start: 0.6789 (ttt) cc_final: 0.6352 (ttp)
REVERT: A  179 ASN cc_start: 0.8360 (t0) cc_final: 0.7959 (t0)
REVERT: A  232 LEU cc_start: 0.8460 (tp) cc_final: 0.8251 (tp)
REVERT: A  256 LYS cc_start: 0.7424 (mmtm) cc_final: 0.6810 (pttp)
  outliers start: 12
  outliers final: 9
  residues processed: 56
  average time/residue: 0.0529
  time to fit residues: 3.8998
Evaluate side-chains
  61 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  439 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 168 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 = 0.3854 r_free = 0.3854 target = 0.155477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.124394 restraints weight = 3812.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.36
r_work: 0.3365 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3435  Z= 0.168
  Angle     :  0.642   7.959   4688  Z= 0.315
  Chirality :  0.043   0.168    568
  Planarity :  0.006   0.062    571
  Dihedral  :  4.875  27.173    481
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 13.64 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.43), residues: 422
  helix:  0.08 (0.29), residues: 315
  sheet:  None (None), residues: 0
  loop : -0.49 (0.73), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 195 
 TYR   0.010   0.001   TYR A 116 
 PHE   0.023   0.002   PHE A 448 
 TRP   0.004   0.001   TRP A  49 
 HIS   0.003   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.17 ( 3433)
  covalent geometry    : angle       0.64140 /  0.32 ( 4683)
  SS BOND              : bond        0.00156 /  0.10 (    1)
  SS BOND              : angle       0.63192 /  0.22 (    2)
  hydrogen bonds       : bond        0.03298 /  2.11 (  195)
  hydrogen bonds       : angle       4.27763 /  3.00 (  573)
  link_NAG-ASN         : bond        0.00217 /  0.14 (    1)
  link_NAG-ASN         : angle       1.09354 /  0.41 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  121 MET cc_start: 0.6897 (ttt) cc_final: 0.6498 (ttp)
REVERT: A  124 LEU cc_start: 0.8282 (mp) cc_final: 0.7982 (mp)
REVERT: A  179 ASN cc_start: 0.8383 (t0) cc_final: 0.7994 (t0)
REVERT: A  232 LEU cc_start: 0.8525 (tp) cc_final: 0.8316 (tp)
REVERT: A  256 LYS cc_start: 0.7469 (mmtm) cc_final: 0.6828 (pttp)
  outliers start: 9
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0519
  time to fit residues: 3.7471
Evaluate side-chains
  61 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  397 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 15 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0000
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 168 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 = 0.4080 r_free = 0.4080 target = 0.170572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.140776 restraints weight = 3815.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 2.24
r_work: 0.3609 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3435  Z= 0.125
  Angle     :  0.621   7.795   4688  Z= 0.304
  Chirality :  0.042   0.173    568
  Planarity :  0.006   0.064    571
  Dihedral  :  4.755  24.766    481
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.37 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.43), residues: 422
  helix:  0.28 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop : -0.60 (0.72), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 365 
 TYR   0.009   0.001   TYR A 332 
 PHE   0.024   0.001   PHE A 448 
 TRP   0.004   0.000   TRP A 330 
 HIS   0.002   0.001   HIS A 369 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.12 ( 3433)
  covalent geometry    : angle       0.62123 /  0.30 ( 4683)
  SS BOND              : bond        0.00216 /  0.14 (    1)
  SS BOND              : angle       0.62076 /  0.22 (    2)
  hydrogen bonds       : bond        0.03084 /  1.98 (  195)
  hydrogen bonds       : angle       4.13214 /  2.88 (  573)
  link_NAG-ASN         : bond        0.00242 /  0.15 (    1)
  link_NAG-ASN         : angle       0.93616 /  0.37 (    3)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8820 (ptpp) cc_final: 0.8339 (ptpp)
REVERT: A  121 MET cc_start: 0.7044 (ttt) cc_final: 0.6641 (ttp)
REVERT: A  124 LEU cc_start: 0.8436 (mp) cc_final: 0.8070 (mp)
REVERT: A  179 ASN cc_start: 0.8338 (t0) cc_final: 0.7975 (t0)
REVERT: A  256 LYS cc_start: 0.7585 (mmtm) cc_final: 0.6968 (pttp)
  outliers start: 10
  outliers final: 10
  residues processed: 56
  average time/residue: 0.0324
  time to fit residues: 2.3970
Evaluate side-chains
  61 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  127 SER
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  397 ASP
Chi-restraints excluded: chain A residue  439 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0870
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 168 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 = 0.4063 r_free = 0.4063 target = 0.169019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.138772 restraints weight = 3927.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.28
r_work: 0.3586 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3435  Z= 0.150
  Angle     :  0.638   7.910   4688  Z= 0.308
  Chirality :  0.042   0.165    568
  Planarity :  0.006   0.062    571
  Dihedral  :  4.706  24.641    481
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.37 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.43), residues: 422
  helix:  0.23 (0.29), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.48 (0.74), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 365 
 TYR   0.009   0.001   TYR A 116 
 PHE   0.022   0.002   PHE A 448 
 TRP   0.003   0.001   TRP A  49 
 HIS   0.003   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.15 ( 3433)
  covalent geometry    : angle       0.63722 /  0.31 ( 4683)
  SS BOND              : bond        0.00206 /  0.13 (    1)
  SS BOND              : angle       0.65291 /  0.23 (    2)
  hydrogen bonds       : bond        0.03197 /  2.05 (  195)
  hydrogen bonds       : angle       4.20090 /  2.95 (  573)
  link_NAG-ASN         : bond        0.00224 /  0.14 (    1)
  link_NAG-ASN         : angle       0.99770 /  0.38 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 878.14 seconds
wall clock time: 15 minutes 54.15 seconds (954.15 seconds total)