Starting phenix.real_space_refine
on Wed Sep 17 07:23:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xza_38791/09_2025/8xza_38791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xza_38791/09_2025/8xza_38791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xza_38791/09_2025/8xza_38791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xza_38791/09_2025/8xza_38791.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xza_38791/09_2025/8xza_38791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xza_38791/09_2025/8xza_38791.map"
  }
  resolution = 4.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.040
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      38      5.16       5
     Cl      1      4.86       5
     C    4202      2.51       5
     N    1083      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6565
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1559
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 13, 'TRANS': 180}
    Chain: "A"
      Number of atoms: 4906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4906
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 571}
    Chain: "B"
      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
    Chain: "A"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 72
          Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.83, per 1000 atoms: 0.28
  Number of scatterers: 6565
  At special positions: 0
  Unit cell: (79, 100, 109, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Cl      1     17.00
     S      38     16.00
     O    1240      8.00
     N    1083      7.00
     C    4202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 487 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 360 " distance=2.02

  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 902 " - " ASN A  53 "
      " NAG A 903 " - " ASN A  90 "
      " NAG A 904 " - " ASN A 298 "
      " NAG A 905 " - " ASN A 431 "
      " NAG A 906 " - " ASN A 545 "
      " NAG B1302 " - " ASN B 343 "
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 446.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      56.2% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'B' and resid 337 through 343
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 403 through 410
      removed outlier: 3.770A  pdb=" N   SER B 408 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.590A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.870A  pdb=" N   GLU A  87 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 88'
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.509A  pdb=" N   HIS A 102 " --> pdb=" O   LYS A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 145 through 154
    Processing helix  chain 'A' and resid 156 through 193
      removed outlier: 3.519A  pdb=" N   ARG A 160 " --> pdb=" O   ASP A 156 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LYS A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
    Processing helix  chain 'A' and resid 197 through 204
    Processing helix  chain 'A' and resid 205 through 207
      No H-bonds generated for 'chain 'A' and resid 205 through 207'
    Processing helix  chain 'A' and resid 219 through 251
      Proline residue:  A 234  - end of helix
    Processing helix  chain 'A' and resid 264 through 266
      No H-bonds generated for 'chain 'A' and resid 264 through 266'
    Processing helix  chain 'A' and resid 274 through 276
      No H-bonds generated for 'chain 'A' and resid 274 through 276'
    Processing helix  chain 'A' and resid 277 through 282
    Processing helix  chain 'A' and resid 292 through 300
    Processing helix  chain 'A' and resid 302 through 316
    Processing helix  chain 'A' and resid 323 through 330
      removed outlier: 3.895A  pdb=" N   TRP A 327 " --> pdb=" O   THR A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 384
      removed outlier: 3.630A  pdb=" N   PHE A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   TYR A 384 " --> pdb=" O   TYR A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
    Processing helix  chain 'A' and resid 398 through 412
      removed outlier: 3.667A  pdb=" N   ALA A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   MET A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 420
      removed outlier: 3.665A  pdb=" N   LEU A 417 " --> pdb=" O   THR A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 444
    Processing helix  chain 'A' and resid 447 through 465
      removed outlier: 4.615A  pdb=" N   PHE A 451 " --> pdb=" O   GLY A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 483
    Processing helix  chain 'A' and resid 497 through 501
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 511 through 532
      removed outlier: 3.602A  pdb=" N   TYR A 515 " --> pdb=" O   PHE A 511 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A 522 " --> pdb=" O   THR A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'A' and resid 546 through 558
      removed outlier: 3.872A  pdb=" N   MET A 556 " --> pdb=" O   ARG A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 571
    Processing helix  chain 'A' and resid 580 through 587
      removed outlier: 3.795A  pdb=" N   PHE A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 598
    Processing helix  chain 'A' and resid 599 through 601
      No H-bonds generated for 'chain 'A' and resid 599 through 601'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 355 through 358
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133
      removed outlier: 3.534A  pdb=" N   LEU A 141 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 262
      removed outlier: 6.710A  pdb=" N   LEU A 261 " --> pdb=" O   VAL A 487 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    299 hydrogen bonds defined for protein.
    864 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: 0.97

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1198
        1.32 -     1.45: 1924
        1.45 -     1.57: 3570
        1.57 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 6752
  Sorted by residual:
  bond pdb=" CA  SER B 438 "
       pdb=" C   SER B 438 "
    ideal  model  delta    sigma   weight residual
    1.522  1.419  0.103 1.08e-02 8.57e+03 9.10e+01
  bond pdb=" CA  ALA B 352 "
       pdb=" C   ALA B 352 "
    ideal  model  delta    sigma   weight residual
    1.530  1.476  0.055 1.08e-02 8.57e+03 2.58e+01
  bond pdb=" CA  ASN B 439 "
       pdb=" C   ASN B 439 "
    ideal  model  delta    sigma   weight residual
    1.522  1.475  0.047 9.30e-03 1.16e+04 2.52e+01
  bond pdb=" CA  ARG B 466 "
       pdb=" C   ARG B 466 "
    ideal  model  delta    sigma   weight residual
    1.524  1.464  0.060 1.25e-02 6.40e+03 2.31e+01
  bond pdb=" CA  SER B 443 "
       pdb=" C   SER B 443 "
    ideal  model  delta    sigma   weight residual
    1.528  1.466  0.061 1.37e-02 5.33e+03 2.00e+01
  ... (remaining 6747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.03: 8906
        3.03 -     6.07: 220
        6.07 -     9.10: 31
        9.10 -    12.13: 3
       12.13 -    15.17: 4
  Bond angle restraints: 9164
  Sorted by residual:
  angle pdb=" N   GLY B 447 "
        pdb=" CA  GLY B 447 "
        pdb=" C   GLY B 447 "
      ideal   model   delta    sigma   weight residual
     111.95  125.46  -13.51 9.50e-01 1.11e+00 2.02e+02
  angle pdb=" N   GLY B 482 "
        pdb=" CA  GLY B 482 "
        pdb=" C   GLY B 482 "
      ideal   model   delta    sigma   weight residual
     110.60  123.34  -12.74 1.46e+00 4.69e-01 7.62e+01
  angle pdb=" N   LYS B 481 "
        pdb=" CA  LYS B 481 "
        pdb=" C   LYS B 481 "
      ideal   model   delta    sigma   weight residual
     111.11  100.80   10.31 1.20e+00 6.94e-01 7.38e+01
  angle pdb=" N   ALA B 352 "
        pdb=" CA  ALA B 352 "
        pdb=" C   ALA B 352 "
      ideal   model   delta    sigma   weight residual
     107.32   93.57   13.75 1.65e+00 3.67e-01 6.94e+01
  angle pdb=" N   PHE B 400 "
        pdb=" CA  PHE B 400 "
        pdb=" C   PHE B 400 "
      ideal   model   delta    sigma   weight residual
     109.63  121.74  -12.11 1.49e+00 4.50e-01 6.61e+01
  ... (remaining 9159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.80: 3803
       23.80 -    47.59: 221
       47.59 -    71.38: 28
       71.38 -    95.18: 9
       95.18 -   118.97: 14
  Dihedral angle restraints: 4075
    sinusoidal: 1746
      harmonic: 2329
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 487 "
           pdb=" CB  CYS B 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.70   72.70     1      1.00e+01 1.00e-02 6.75e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.40   48.60     1      1.00e+01 1.00e-02 3.25e+01
  dihedral pdb=" CA  MET A  62 "
           pdb=" C   MET A  62 "
           pdb=" N   ASN A  63 "
           pdb=" CA  ASN A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.82   26.18     0      5.00e+00 4.00e-02 2.74e+01
  ... (remaining 4072 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 822
       0.075 -    0.150: 124
       0.150 -    0.225: 16
       0.225 -    0.300: 3
       0.300 -    0.375: 3
  Chirality restraints: 968
  Sorted by residual:
  chirality pdb=" C1  NAG A 902 "
            pdb=" ND2 ASN A  53 "
            pdb=" C2  NAG A 902 "
            pdb=" O5  NAG A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.52e+00
  chirality pdb=" C1  NAG A 904 "
            pdb=" ND2 ASN A 298 "
            pdb=" C2  NAG A 904 "
            pdb=" O5  NAG A 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.28e+00
  chirality pdb=" CA  TRP B 353 "
            pdb=" N   TRP B 353 "
            pdb=" C   TRP B 353 "
            pdb=" CB  TRP B 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.34e+00
  ... (remaining 965 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B1301 "    0.297 2.00e-02 2.50e+03   2.53e-01 8.02e+02
        pdb=" C7  NAG B1301 "   -0.069 2.00e-02 2.50e+03
        pdb=" C8  NAG B1301 "   -0.018 2.00e-02 2.50e+03
        pdb=" N2  NAG B1301 "   -0.425 2.00e-02 2.50e+03
        pdb=" O7  NAG B1301 "    0.215 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 350 "   -0.043 2.00e-02 2.50e+03   8.82e-02 7.78e+01
        pdb=" C   VAL B 350 "    0.152 2.00e-02 2.50e+03
        pdb=" O   VAL B 350 "   -0.059 2.00e-02 2.50e+03
        pdb=" N   TYR B 351 "   -0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 345 "    0.031 2.00e-02 2.50e+03   6.23e-02 3.88e+01
        pdb=" C   THR B 345 "   -0.108 2.00e-02 2.50e+03
        pdb=" O   THR B 345 "    0.040 2.00e-02 2.50e+03
        pdb=" N   ARG B 346 "    0.037 2.00e-02 2.50e+03
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        1.21 -     1.95: 4
        1.95 -     2.69: 278
        2.69 -     3.42: 10143
        3.42 -     4.16: 16088
        4.16 -     4.90: 27724
  Nonbonded interactions: 54237
  Sorted by model distance:
  nonbonded pdb=" CD2 TYR B 351 "
            pdb=" O   TRP B 452 "
     model   vdw
     1.212 3.340
  nonbonded pdb=" CZ3 TRP B 353 "
            pdb=" CB  ARG B 355 "
     model   vdw
     1.659 3.740
  nonbonded pdb=" CE2 TYR B 351 "
            pdb=" O   TRP B 452 "
     model   vdw
     1.746 3.340
  nonbonded pdb=" OH  TYR A 242 "
            pdb=" O   LEU A 594 "
     model   vdw
     1.927 3.040
  nonbonded pdb=" OG  SER B 349 "
            pdb=" CE2 TYR B 351 "
     model   vdw
     1.982 3.340
  ... (remaining 54232 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.330
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.240
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
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      :  0.007   0.103   6763  Z= 0.430
  Angle     :  1.111  15.168   9192  Z= 0.643
  Chirality :  0.058   0.375    968
  Planarity :  0.010   0.253   1168
  Dihedral  : 16.313 118.973   2566
  Min Nonbonded Distance : 1.212

Molprobity Statistics.
  All-atom Clashscore : 30.95
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  8.02 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.02 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -1.65 (0.28), residues: 786
  helix: -0.42 (0.25), residues: 393
  sheet: -0.89 (0.99), residues: 31
  loop : -1.85 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 558 
 TYR   0.055   0.003   TYR A 453 
 PHE   0.030   0.003   PHE A 437 
 TRP   0.029   0.003   TRP A 164 
 HIS   0.008   0.001   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00675 ( 6752)
  covalent geometry    : angle       1.09875 ( 9164)
  SS BOND              : bond        0.00548 (    5)
  SS BOND              : angle       1.79302 (   10)
  hydrogen bonds       : bond        0.14353 (  299)
  hydrogen bonds       : angle       6.79056 (  864)
  link_NAG-ASN         : bond        0.00904 (    6)
  link_NAG-ASN         : angle       3.65526 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.7243 (mp0) cc_final: 0.6369 (tp30)
REVERT: B  514 PHE cc_start: 0.6054 (m-80) cc_final: 0.5764 (m-10)
REVERT: A  248 MET cc_start: 0.7022 (ptm) cc_final: 0.6782 (ppp)
REVERT: A  455 LEU cc_start: 0.9450 (mt) cc_final: 0.9070 (mt)
REVERT: A  458 TRP cc_start: 0.7185 (m100) cc_final: 0.6846 (m100)
REVERT: A  557 LEU cc_start: 0.8950 (mt) cc_final: 0.8526 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0936
  time to fit residues: 18.6483
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.0170
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0050
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4832

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN
B 474 GLN
B 492 GLN
A  33 ASN
A  42 GLN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.128243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.104654 restraints weight = 21536.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.107903 restraints weight = 11900.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.110088 restraints weight = 7705.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.111391 restraints weight = 5624.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.112442 restraints weight = 4553.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6763  Z= 0.168
  Angle     :  0.766   9.150   9192  Z= 0.386
  Chirality :  0.050   0.385    968
  Planarity :  0.005   0.044   1168
  Dihedral  : 10.305 108.546   1016
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 16.76
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.06 %
    Favored  : 93.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -1.32 (0.29), residues: 786
  helix: -0.29 (0.25), residues: 408
  sheet: -0.03 (0.94), residues: 30
  loop : -1.60 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 466 
 TYR   0.044   0.002   TYR A 453 
 PHE   0.017   0.002   PHE B 347 
 TRP   0.043   0.002   TRP B 353 
 HIS   0.006   0.001   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6752)
  covalent geometry    : angle       0.75456 ( 9164)
  SS BOND              : bond        0.00193 (    5)
  SS BOND              : angle       1.09390 (   10)
  hydrogen bonds       : bond        0.04674 (  299)
  hydrogen bonds       : angle       5.41472 (  864)
  link_NAG-ASN         : bond        0.00651 (    6)
  link_NAG-ASN         : angle       2.97377 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7416 (mtpt)
REVERT: B  499 THR cc_start: 0.8585 (p) cc_final: 0.8319 (p)
REVERT: A   79 MET cc_start: 0.8794 (tpp) cc_final: 0.8280 (tpp)
REVERT: A  100 LEU cc_start: 0.8651 (mt) cc_final: 0.8392 (mt)
REVERT: A  248 MET cc_start: 0.7123 (ptm) cc_final: 0.6845 (ppp)
REVERT: A  453 TYR cc_start: 0.6642 (m-80) cc_final: 0.6252 (m-80)
REVERT: A  455 LEU cc_start: 0.9557 (mt) cc_final: 0.9123 (mt)
REVERT: A  458 TRP cc_start: 0.7222 (m100) cc_final: 0.6792 (m100)
REVERT: A  479 MET cc_start: 0.8952 (ppp) cc_final: 0.8704 (ppp)
REVERT: A  516 THR cc_start: 0.8902 (p) cc_final: 0.8379 (p)
REVERT: A  557 LEU cc_start: 0.8979 (mt) cc_final: 0.8614 (mt)
REVERT: A  588 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7698 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0782
  time to fit residues: 14.9774
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 47 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  33 ASN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 HIS
A 525 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.125688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.102140 restraints weight = 21259.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.105315 restraints weight = 11821.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.107411 restraints weight = 7737.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.108834 restraints weight = 5707.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.109683 restraints weight = 4598.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6763  Z= 0.156
  Angle     :  0.719   9.255   9192  Z= 0.361
  Chirality :  0.048   0.340    968
  Planarity :  0.005   0.044   1168
  Dihedral  :  8.869 101.670   1016
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.47 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -1.12 (0.29), residues: 786
  helix: -0.12 (0.25), residues: 403
  sheet:  0.09 (0.93), residues: 30
  loop : -1.51 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 305 
 TYR   0.039   0.002   TYR A 453 
 PHE   0.019   0.002   PHE A 437 
 TRP   0.030   0.002   TRP A 270 
 HIS   0.005   0.001   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6752)
  covalent geometry    : angle       0.70638 ( 9164)
  SS BOND              : bond        0.00212 (    5)
  SS BOND              : angle       1.40812 (   10)
  hydrogen bonds       : bond        0.04331 (  299)
  hydrogen bonds       : angle       5.18755 (  864)
  link_NAG-ASN         : bond        0.00850 (    6)
  link_NAG-ASN         : angle       2.95613 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 LYS cc_start: 0.7876 (mtmt) cc_final: 0.7520 (mtpt)
REVERT: B  499 THR cc_start: 0.8642 (p) cc_final: 0.8357 (p)
REVERT: A   79 MET cc_start: 0.8830 (tpp) cc_final: 0.8322 (tpp)
REVERT: A  100 LEU cc_start: 0.8669 (mt) cc_final: 0.8456 (mt)
REVERT: A  151 MET cc_start: 0.6718 (tpt) cc_final: 0.5857 (tpp)
REVERT: A  248 MET cc_start: 0.7267 (ptm) cc_final: 0.6971 (ppp)
REVERT: A  322 MET cc_start: 0.8338 (mmm) cc_final: 0.7244 (mmt)
REVERT: A  440 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7806 (mmtm)
REVERT: A  453 TYR cc_start: 0.5969 (m-80) cc_final: 0.5722 (m-80)
REVERT: A  455 LEU cc_start: 0.9594 (mt) cc_final: 0.9343 (mt)
REVERT: A  458 TRP cc_start: 0.7159 (m100) cc_final: 0.6569 (m100)
REVERT: A  479 MET cc_start: 0.8926 (ppp) cc_final: 0.8664 (ppp)
REVERT: A  516 THR cc_start: 0.8952 (p) cc_final: 0.8406 (p)
REVERT: A  557 LEU cc_start: 0.8982 (mt) cc_final: 0.8586 (mt)
REVERT: A  567 LEU cc_start: 0.9033 (tp) cc_final: 0.8823 (tp)
REVERT: A  588 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7848 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0864
  time to fit residues: 16.1799
Evaluate side-chains
  100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
A 551 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.124701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.101281 restraints weight = 21694.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.104461 restraints weight = 12101.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.106529 restraints weight = 7913.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.107773 restraints weight = 5828.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.108890 restraints weight = 4755.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6763  Z= 0.157
  Angle     :  0.716   9.730   9192  Z= 0.357
  Chirality :  0.048   0.347    968
  Planarity :  0.005   0.048   1168
  Dihedral  :  8.546  97.924   1016
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -0.99 (0.29), residues: 786
  helix: -0.03 (0.26), residues: 400
  sheet: -0.22 (0.85), residues: 31
  loop : -1.37 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 305 
 TYR   0.035   0.002   TYR A 453 
 PHE   0.021   0.002   PHE A 437 
 TRP   0.037   0.002   TRP B 353 
 HIS   0.003   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6752)
  covalent geometry    : angle       0.70363 ( 9164)
  SS BOND              : bond        0.00217 (    5)
  SS BOND              : angle       1.47914 (   10)
  hydrogen bonds       : bond        0.04222 (  299)
  hydrogen bonds       : angle       5.12671 (  864)
  link_NAG-ASN         : bond        0.00640 (    6)
  link_NAG-ASN         : angle       2.97667 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7480 (mtpt)
REVERT: B  499 THR cc_start: 0.8548 (p) cc_final: 0.8277 (p)
REVERT: A  100 LEU cc_start: 0.8634 (mt) cc_final: 0.8422 (mt)
REVERT: A  151 MET cc_start: 0.7007 (tpt) cc_final: 0.6206 (tpp)
REVERT: A  248 MET cc_start: 0.7415 (ptm) cc_final: 0.7120 (ppp)
REVERT: A  302 ASP cc_start: 0.7956 (t70) cc_final: 0.7722 (t70)
REVERT: A  382 MET cc_start: 0.8960 (mtp) cc_final: 0.8634 (mtm)
REVERT: A  453 TYR cc_start: 0.5548 (m-80) cc_final: 0.4866 (m-80)
REVERT: A  455 LEU cc_start: 0.9558 (mt) cc_final: 0.9352 (mt)
REVERT: A  458 TRP cc_start: 0.7247 (m100) cc_final: 0.6943 (m100)
REVERT: A  515 TYR cc_start: 0.7566 (t80) cc_final: 0.7254 (t80)
REVERT: A  557 LEU cc_start: 0.8972 (mt) cc_final: 0.8542 (mt)
REVERT: A  588 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7859 (mm-30)
REVERT: A  594 LEU cc_start: 0.7708 (mt) cc_final: 0.7477 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0779
  time to fit residues: 14.0324
Evaluate side-chains
  100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  42 GLN
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 GLN
A 598 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.122485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.098607 restraints weight = 21798.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.101747 restraints weight = 11819.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.103835 restraints weight = 7632.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.105110 restraints weight = 5588.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.106141 restraints weight = 4528.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6763  Z= 0.167
  Angle     :  0.715   9.643   9192  Z= 0.357
  Chirality :  0.049   0.352    968
  Planarity :  0.004   0.048   1168
  Dihedral  :  8.329  96.048   1016
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -0.96 (0.29), residues: 786
  helix: -0.09 (0.25), residues: 411
  sheet: -0.54 (0.92), residues: 29
  loop : -1.23 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 457 
 TYR   0.037   0.002   TYR A  50 
 PHE   0.021   0.002   PHE A 437 
 TRP   0.034   0.002   TRP B 353 
 HIS   0.005   0.001   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6752)
  covalent geometry    : angle       0.70340 ( 9164)
  SS BOND              : bond        0.00373 (    5)
  SS BOND              : angle       1.37340 (   10)
  hydrogen bonds       : bond        0.04043 (  299)
  hydrogen bonds       : angle       5.15306 (  864)
  link_NAG-ASN         : bond        0.00636 (    6)
  link_NAG-ASN         : angle       2.85959 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 LYS cc_start: 0.7820 (mtmt) cc_final: 0.7412 (mtpt)
REVERT: B  499 THR cc_start: 0.8556 (p) cc_final: 0.8252 (p)
REVERT: A  151 MET cc_start: 0.6852 (tpt) cc_final: 0.5973 (tpp)
REVERT: A  248 MET cc_start: 0.7420 (ptm) cc_final: 0.7179 (ppp)
REVERT: A  440 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7994 (ttpt)
REVERT: A  446 VAL cc_start: 0.8709 (m) cc_final: 0.8393 (p)
REVERT: A  451 PHE cc_start: 0.9095 (t80) cc_final: 0.8829 (t80)
REVERT: A  453 TYR cc_start: 0.5378 (m-80) cc_final: 0.4722 (m-80)
REVERT: A  455 LEU cc_start: 0.9617 (mt) cc_final: 0.9328 (mt)
REVERT: A  458 TRP cc_start: 0.7283 (m100) cc_final: 0.7067 (m100)
REVERT: A  557 LEU cc_start: 0.9063 (mt) cc_final: 0.8635 (mt)
REVERT: A  588 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7958 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0803
  time to fit residues: 14.4597
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.0000
   chunk 7 optimal weight:    0.0270
   chunk 4 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0470
   chunk 17 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.2140

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 GLN
A 387 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.125918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.102623 restraints weight = 21392.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.105822 restraints weight = 11770.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.107947 restraints weight = 7590.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.109357 restraints weight = 5541.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.110028 restraints weight = 4444.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6763  Z= 0.136
  Angle     :  0.720  11.424   9192  Z= 0.355
  Chirality :  0.050   0.492    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  7.825  89.524   1016
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -0.76 (0.29), residues: 786
  helix:  0.06 (0.26), residues: 403
  sheet: -0.18 (0.93), residues: 29
  loop : -1.12 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 457 
 TYR   0.046   0.002   TYR A  50 
 PHE   0.020   0.002   PHE A  32 
 TRP   0.038   0.002   TRP B 353 
 HIS   0.005   0.001   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6752)
  covalent geometry    : angle       0.69998 ( 9164)
  SS BOND              : bond        0.00149 (    5)
  SS BOND              : angle       1.09743 (   10)
  hydrogen bonds       : bond        0.03837 (  299)
  hydrogen bonds       : angle       5.04139 (  864)
  link_NAG-ASN         : bond        0.00562 (    6)
  link_NAG-ASN         : angle       3.83067 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  424 LYS cc_start: 0.6853 (ttmt) cc_final: 0.6537 (tptt)
REVERT: B  499 THR cc_start: 0.8420 (p) cc_final: 0.8141 (p)
REVERT: A  151 MET cc_start: 0.6770 (tpt) cc_final: 0.5856 (tpp)
REVERT: A  248 MET cc_start: 0.7412 (ptm) cc_final: 0.7164 (ppp)
REVERT: A  274 TRP cc_start: 0.8064 (m-10) cc_final: 0.7777 (m-10)
REVERT: A  302 ASP cc_start: 0.8040 (t70) cc_final: 0.7833 (t70)
REVERT: A  405 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7611 (mm-30)
REVERT: A  440 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7895 (mmtm)
REVERT: A  446 VAL cc_start: 0.8824 (m) cc_final: 0.8513 (p)
REVERT: A  453 TYR cc_start: 0.4856 (m-80) cc_final: 0.4499 (m-80)
REVERT: A  525 HIS cc_start: 0.8133 (t70) cc_final: 0.7754 (t-90)
REVERT: A  557 LEU cc_start: 0.9055 (mt) cc_final: 0.8641 (mt)
REVERT: A  588 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7913 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0787
  time to fit residues: 15.0813
Evaluate side-chains
  99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 46 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   chunk 44 optimal weight:    0.1980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 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 = 0.4068 r_free = 0.4068 target = 0.121109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.097279 restraints weight = 20673.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.100491 restraints weight = 11435.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.102669 restraints weight = 7437.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.103940 restraints weight = 5430.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.105001 restraints weight = 4403.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6763  Z= 0.157
  Angle     :  0.765  11.522   9192  Z= 0.381
  Chirality :  0.050   0.417    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  7.468  78.756   1016
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.83 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -0.75 (0.29), residues: 786
  helix: -0.01 (0.25), residues: 405
  sheet: -0.23 (0.94), residues: 29
  loop : -0.99 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.043   0.002   TYR A  50 
 PHE   0.025   0.002   PHE A 326 
 TRP   0.038   0.002   TRP B 353 
 HIS   0.005   0.001   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6752)
  covalent geometry    : angle       0.75220 ( 9164)
  SS BOND              : bond        0.00288 (    5)
  SS BOND              : angle       1.61129 (   10)
  hydrogen bonds       : bond        0.04210 (  299)
  hydrogen bonds       : angle       5.16162 (  864)
  link_NAG-ASN         : bond        0.00587 (    6)
  link_NAG-ASN         : angle       3.12122 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  499 THR cc_start: 0.8474 (p) cc_final: 0.8212 (p)
REVERT: A  151 MET cc_start: 0.6862 (tpt) cc_final: 0.6641 (tpp)
REVERT: A  248 MET cc_start: 0.7494 (ptm) cc_final: 0.7272 (ppp)
REVERT: A  302 ASP cc_start: 0.8146 (t70) cc_final: 0.7922 (t70)
REVERT: A  405 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7626 (mm-30)
REVERT: A  440 LYS cc_start: 0.8200 (tmtt) cc_final: 0.7898 (mmtm)
REVERT: A  446 VAL cc_start: 0.8860 (m) cc_final: 0.8601 (p)
REVERT: A  453 TYR cc_start: 0.4806 (m-80) cc_final: 0.4577 (m-80)
REVERT: A  525 HIS cc_start: 0.8111 (t70) cc_final: 0.7833 (t-90)
REVERT: A  557 LEU cc_start: 0.9076 (mt) cc_final: 0.8741 (mt)
REVERT: A  588 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8000 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0656
  time to fit residues: 12.2134
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 49 optimal weight:    0.1980
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0570
   chunk 63 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0770
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 GLN
A 598 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.122531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.099723 restraints weight = 20568.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.102919 restraints weight = 11215.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.105137 restraints weight = 7252.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.106609 restraints weight = 5262.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.107571 restraints weight = 4184.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6763  Z= 0.139
  Angle     :  0.748  10.423   9192  Z= 0.368
  Chirality :  0.049   0.391    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  6.743  55.398   1016
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.34 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.16 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -0.76 (0.29), residues: 786
  helix:  0.03 (0.25), residues: 404
  sheet: -0.09 (0.94), residues: 29
  loop : -1.08 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 305 
 TYR   0.036   0.002   TYR A  50 
 PHE   0.020   0.002   PHE A  32 
 TRP   0.036   0.002   TRP B 353 
 HIS   0.006   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6752)
  covalent geometry    : angle       0.73322 ( 9164)
  SS BOND              : bond        0.00548 (    5)
  SS BOND              : angle       1.31795 (   10)
  hydrogen bonds       : bond        0.03942 (  299)
  hydrogen bonds       : angle       5.01263 (  864)
  link_NAG-ASN         : bond        0.00584 (    6)
  link_NAG-ASN         : angle       3.34696 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  499 THR cc_start: 0.8438 (p) cc_final: 0.8163 (p)
REVERT: B  504 HIS cc_start: 0.8644 (m90) cc_final: 0.8268 (m90)
REVERT: A   23 GLU cc_start: 0.8306 (mp0) cc_final: 0.7834 (mp0)
REVERT: A  151 MET cc_start: 0.6849 (tpt) cc_final: 0.6566 (tpp)
REVERT: A  302 ASP cc_start: 0.8043 (t70) cc_final: 0.7820 (t70)
REVERT: A  407 MET cc_start: 0.9253 (mmt) cc_final: 0.9013 (mmt)
REVERT: A  440 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7950 (mmtm)
REVERT: A  451 PHE cc_start: 0.8992 (t80) cc_final: 0.8756 (t80)
REVERT: A  453 TYR cc_start: 0.5000 (m-80) cc_final: 0.4782 (m-80)
REVERT: A  458 TRP cc_start: 0.7078 (m100) cc_final: 0.6713 (m100)
REVERT: A  525 HIS cc_start: 0.8061 (t70) cc_final: 0.7763 (t-90)
REVERT: A  557 LEU cc_start: 0.9073 (mt) cc_final: 0.8718 (mt)
REVERT: A  588 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7953 (mm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0682
  time to fit residues: 12.7074
Evaluate side-chains
  101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 74 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 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 = 0.4170 r_free = 0.4170 target = 0.124061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.100077 restraints weight = 21679.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.103245 restraints weight = 11813.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.105418 restraints weight = 7690.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.106826 restraints weight = 5661.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.107745 restraints weight = 4567.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.4668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6763  Z= 0.161
  Angle     :  0.783  10.107   9192  Z= 0.390
  Chirality :  0.050   0.388    968
  Planarity :  0.004   0.049   1168
  Dihedral  :  6.441  55.624   1016
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 17.78
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.09 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -0.81 (0.30), residues: 786
  helix: -0.08 (0.25), residues: 409
  sheet: -0.42 (0.98), residues: 30
  loop : -0.99 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 392 
 TYR   0.060   0.002   TYR A  50 
 PHE   0.021   0.002   PHE A 229 
 TRP   0.030   0.002   TRP B 353 
 HIS   0.005   0.001   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6752)
  covalent geometry    : angle       0.76832 ( 9164)
  SS BOND              : bond        0.00343 (    5)
  SS BOND              : angle       1.32839 (   10)
  hydrogen bonds       : bond        0.04149 (  299)
  hydrogen bonds       : angle       5.21244 (  864)
  link_NAG-ASN         : bond        0.00518 (    6)
  link_NAG-ASN         : angle       3.37761 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7795 (mtpt)
REVERT: B  499 THR cc_start: 0.8475 (p) cc_final: 0.8204 (p)
REVERT: A   64 GLU cc_start: 0.8921 (mp0) cc_final: 0.8708 (mp0)
REVERT: A  151 MET cc_start: 0.6621 (tpt) cc_final: 0.6316 (tpp)
REVERT: A  302 ASP cc_start: 0.8126 (t70) cc_final: 0.7897 (t70)
REVERT: A  407 MET cc_start: 0.9242 (mmt) cc_final: 0.8921 (mmt)
REVERT: A  451 PHE cc_start: 0.9099 (t80) cc_final: 0.8890 (t80)
REVERT: A  458 TRP cc_start: 0.7144 (m100) cc_final: 0.6719 (m100)
REVERT: A  525 HIS cc_start: 0.8241 (t70) cc_final: 0.8011 (t-90)
REVERT: A  557 LEU cc_start: 0.9120 (mt) cc_final: 0.8828 (mt)
REVERT: A  588 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8062 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0564
  time to fit residues: 10.2574
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0170
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 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 = 0.4072 r_free = 0.4072 target = 0.121229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.098601 restraints weight = 19901.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.101743 restraints weight = 10857.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.103943 restraints weight = 6960.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.105395 restraints weight = 4999.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.106237 restraints weight = 3936.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.4914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6763  Z= 0.155
  Angle     :  0.765  10.221   9192  Z= 0.383
  Chirality :  0.050   0.379    968
  Planarity :  0.004   0.055   1168
  Dihedral  :  6.259  55.913   1016
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.09 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -0.80 (0.30), residues: 786
  helix: -0.07 (0.25), residues: 405
  sheet: -0.19 (1.00), residues: 30
  loop : -1.01 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 305 
 TYR   0.048   0.002   TYR A  50 
 PHE   0.032   0.002   PHE B 375 
 TRP   0.031   0.002   TRP A 202 
 HIS   0.004   0.001   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6752)
  covalent geometry    : angle       0.75028 ( 9164)
  SS BOND              : bond        0.00248 (    5)
  SS BOND              : angle       1.30532 (   10)
  hydrogen bonds       : bond        0.04042 (  299)
  hydrogen bonds       : angle       5.17994 (  864)
  link_NAG-ASN         : bond        0.00573 (    6)
  link_NAG-ASN         : angle       3.33191 (   18)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7658 (mtpt)
REVERT: B  499 THR cc_start: 0.8396 (p) cc_final: 0.8106 (p)
REVERT: A   23 GLU cc_start: 0.8309 (mp0) cc_final: 0.7794 (mp0)
REVERT: A   63 ASN cc_start: 0.8539 (m-40) cc_final: 0.8280 (m-40)
REVERT: A   64 GLU cc_start: 0.8736 (mp0) cc_final: 0.8483 (mp0)
REVERT: A  151 MET cc_start: 0.6574 (tpt) cc_final: 0.5538 (tpp)
REVERT: A  196 GLU cc_start: 0.8248 (tp30) cc_final: 0.7991 (tp30)
REVERT: A  302 ASP cc_start: 0.8090 (t70) cc_final: 0.7450 (t70)
REVERT: A  407 MET cc_start: 0.9224 (mmt) cc_final: 0.8962 (mmt)
REVERT: A  451 PHE cc_start: 0.9055 (t80) cc_final: 0.8853 (t80)
REVERT: A  453 TYR cc_start: 0.5541 (m-10) cc_final: 0.4621 (m-10)
REVERT: A  458 TRP cc_start: 0.7128 (m100) cc_final: 0.6440 (m100)
REVERT: A  525 HIS cc_start: 0.8199 (t70) cc_final: 0.7940 (t-90)
REVERT: A  557 LEU cc_start: 0.9086 (mt) cc_final: 0.8775 (mt)
REVERT: A  588 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8045 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0659
  time to fit residues: 12.0706
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    0.1980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 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 = 0.4074 r_free = 0.4074 target = 0.121254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.097648 restraints weight = 20642.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.100841 restraints weight = 11289.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.103022 restraints weight = 7274.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.104525 restraints weight = 5277.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.105356 restraints weight = 4181.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.5070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6763  Z= 0.150
  Angle     :  0.790  18.725   9192  Z= 0.391
  Chirality :  0.050   0.379    968
  Planarity :  0.004   0.048   1168
  Dihedral  :  6.169  56.839   1016
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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 aren not related in a simple way.
  whole: -0.85 (0.30), residues: 786
  helix: -0.09 (0.25), residues: 399
  sheet: -0.09 (1.00), residues: 30
  loop : -1.07 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 305 
 TYR   0.045   0.002   TYR A  50 
 PHE   0.032   0.002   PHE B 375 
 TRP   0.060   0.002   TRP A 476 
 HIS   0.004   0.001   HIS A 525 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6752)
  covalent geometry    : angle       0.77850 ( 9164)
  SS BOND              : bond        0.00240 (    5)
  SS BOND              : angle       1.22399 (   10)
  hydrogen bonds       : bond        0.04073 (  299)
  hydrogen bonds       : angle       5.27634 (  864)
  link_NAG-ASN         : bond        0.00569 (    6)
  link_NAG-ASN         : angle       3.06221 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1406.90 seconds
wall clock time: 25 minutes 6.56 seconds (1506.56 seconds total)