Starting phenix.real_space_refine
on Sat May 10 17:24:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xza_38791/05_2025/8xza_38791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xza_38791/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xza_38791/05_2025/8xza_38791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xza_38791/05_2025/8xza_38791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xza_38791/05_2025/8xza_38791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xza_38791/05_2025/8xza_38791.cif"
  }
  resolution = 4.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.91, per 1000 atoms: 0.75
  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: 1.66
  Conformation dependent library (CDL) restraints added in 978.8 milliseconds
  

  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: 0.65
  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: 1.70

  Time building geometry restraints manager: 1.95 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.270
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.860
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.029   0.003   TRP A 164 
 HIS   0.008   0.001   HIS A 264 
 PHE   0.030   0.003   PHE A 437 
 TYR   0.055   0.003   TYR A 453 
 ARG   0.004   0.001   ARG A 558 

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

*********************** 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  : 0.717 
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: 0.5758 (m-10)
REVERT: A  100 LEU cc_start: 0.8461 (mt) cc_final: 0.8260 (mt)
REVERT: A  248 MET cc_start: 0.7022 (ptm) cc_final: 0.6781 (ppp)
REVERT: A  455 LEU cc_start: 0.9450 (mt) cc_final: 0.9067 (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: 0.8523 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2050
  time to fit residues: 40.5392
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  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0770
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.9540

-------------------------------------------------------------------------------
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 = 0.4178 r_free = 0.4178 target = 0.125572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.101999 restraints weight = 21162.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.105123 restraints weight = 11791.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.107236 restraints weight = 7711.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2053

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= 0.177
  Angle     :  0.776   9.304   9192  Z= 0.393
  Chirality :  0.050   0.385    968
  Planarity :  0.005   0.044   1168
  Dihedral  : 10.262 108.064   1016
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 18.95
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.47 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.64 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.29), residues: 786
  helix: -0.17 (0.25), residues: 397
  sheet: -0.35 (0.93), residues: 31
  loop : -1.68 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.003   TRP B 353 
 HIS   0.006   0.001   HIS A 264 
 PHE   0.017   0.002   PHE B 347 
 TYR   0.047   0.003   TYR A 453 
 ARG   0.004   0.001   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00689 (    6)
  link_NAG-ASN         : angle       2.99451 (   18)
  hydrogen bonds       : bond        0.04680 (  299)
  hydrogen bonds       : angle       5.40201 (  864)
  SS BOND              : bond        0.00272 (    5)
  SS BOND              : angle       1.20074 (   10)
  covalent geometry    : bond        0.00396 ( 6752)
  covalent geometry    : angle       0.76520 ( 9164)

*********************** 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  : 0.693 
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: 0.7796 (mtmt) cc_final: 0.7299 (mtpt)
REVERT: B  499 THR cc_start: 0.8586 (p) cc_final: 0.8334 (p)
REVERT: A   79 MET cc_start: 0.8819 (tpp) cc_final: 0.8331 (tpp)
REVERT: A  100 LEU cc_start: 0.8722 (mt) cc_final: 0.8458 (mt)
REVERT: A  123 MET cc_start: 0.8248 (mtm) cc_final: 0.8006 (mtm)
REVERT: A  167 TRP cc_start: 0.4146 (m-90) cc_final: 0.3937 (t-100)
REVERT: A  248 MET cc_start: 0.7158 (ptm) cc_final: 0.6878 (ppp)
REVERT: A  455 LEU cc_start: 0.9567 (mt) cc_final: 0.9151 (mt)
REVERT: A  458 TRP cc_start: 0.7273 (m100) cc_final: 0.6810 (m100)
REVERT: A  479 MET cc_start: 0.8975 (ppp) cc_final: 0.8704 (ppp)
REVERT: A  516 THR cc_start: 0.8998 (p) cc_final: 0.8500 (p)
REVERT: A  557 LEU cc_start: 0.8958 (mt) cc_final: 0.8566 (mt)
REVERT: A  567 LEU cc_start: 0.9031 (tp) cc_final: 0.8815 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 140
  average time/residue: 0.1712
  time to fit residues: 32.3228
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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  33 ASN
A  42 GLN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.118332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.094275 restraints weight = 21660.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.097296 restraints weight = 11973.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.099305 restraints weight = 7845.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   6763  Z= 0.253
  Angle     :  0.817  10.661   9192  Z= 0.416
  Chirality :  0.051   0.327    968
  Planarity :  0.005   0.045   1168
  Dihedral  :  9.539  98.811   1016
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 22.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.23 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.63 %
    Favored  : 94.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.29), residues: 786
  helix: -0.35 (0.25), residues: 408
  sheet: -0.26 (0.98), residues: 29
  loop : -1.49 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B 353 
 HIS   0.008   0.001   HIS A 264 
 PHE   0.023   0.002   PHE B 347 
 TYR   0.075   0.003   TYR A 453 
 ARG   0.005   0.001   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00660 (    6)
  link_NAG-ASN         : angle       3.09138 (   18)
  hydrogen bonds       : bond        0.04855 (  299)
  hydrogen bonds       : angle       5.46962 (  864)
  SS BOND              : bond        0.00377 (    5)
  SS BOND              : angle       1.60133 (   10)
  covalent geometry    : bond        0.00556 ( 6752)
  covalent geometry    : angle       0.80547 ( 9164)

*********************** 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
  127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.757 
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: 0.7764 (mtmt) cc_final: 0.7132 (mtpt)
REVERT: B  499 THR cc_start: 0.8629 (p) cc_final: 0.8376 (p)
REVERT: A  100 LEU cc_start: 0.8714 (mt) cc_final: 0.8443 (mt)
REVERT: A  151 MET cc_start: 0.6401 (tpt) cc_final: 0.5826 (tpp)
REVERT: A  189 MET cc_start: 0.8845 (tmm) cc_final: 0.8412 (tmm)
REVERT: A  248 MET cc_start: 0.7448 (ptm) cc_final: 0.7206 (ppp)
REVERT: A  382 MET cc_start: 0.8776 (mtp) cc_final: 0.8502 (mtm)
REVERT: A  458 TRP cc_start: 0.7231 (m100) cc_final: 0.6771 (m100)
REVERT: A  479 MET cc_start: 0.9036 (ppp) cc_final: 0.8816 (ppp)
REVERT: A  516 THR cc_start: 0.9063 (p) cc_final: 0.8522 (p)
REVERT: A  567 LEU cc_start: 0.9042 (tp) cc_final: 0.8786 (tp)
REVERT: A  588 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8119 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1726
  time to fit residues: 29.9915
Evaluate side-chains
  96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0370
   chunk 9 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.6858

-------------------------------------------------------------------------------
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 492 GLN
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 ASN
** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 HIS
A 525 HIS
A 551 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.121748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.098013 restraints weight = 21560.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.101094 restraints weight = 11951.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.103177 restraints weight = 7763.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6763  Z= 0.165
  Angle     :  0.741   9.726   9192  Z= 0.370
  Chirality :  0.049   0.348    968
  Planarity :  0.005   0.049   1168
  Dihedral  :  8.660  91.059   1016
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.71 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.60 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.29), residues: 786
  helix: -0.24 (0.25), residues: 402
  sheet: -0.37 (0.94), residues: 29
  loop : -1.41 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 353 
 HIS   0.008   0.001   HIS A 264 
 PHE   0.024   0.002   PHE B 456 
 TYR   0.043   0.002   TYR A 453 
 ARG   0.007   0.001   ARG A 305 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00695 (    6)
  link_NAG-ASN         : angle       3.03522 (   18)
  hydrogen bonds       : bond        0.04443 (  299)
  hydrogen bonds       : angle       5.37631 (  864)
  SS BOND              : bond        0.00343 (    5)
  SS BOND              : angle       1.40435 (   10)
  covalent geometry    : bond        0.00354 ( 6752)
  covalent geometry    : angle       0.72811 ( 9164)

*********************** 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
  128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  499 THR cc_start: 0.8480 (p) cc_final: 0.8190 (p)
REVERT: A  151 MET cc_start: 0.6715 (tpt) cc_final: 0.6353 (tpp)
REVERT: A  164 TRP cc_start: 0.6311 (m-90) cc_final: 0.5827 (m-90)
REVERT: A  248 MET cc_start: 0.7449 (ptm) cc_final: 0.7191 (ppp)
REVERT: A  322 MET cc_start: 0.7733 (mtt) cc_final: 0.7252 (mtt)
REVERT: A  453 TYR cc_start: 0.6018 (m-80) cc_final: 0.5682 (m-80)
REVERT: A  522 PHE cc_start: 0.8825 (m-10) cc_final: 0.8538 (m-10)
REVERT: A  557 LEU cc_start: 0.8997 (mm) cc_final: 0.8715 (mm)
REVERT: A  567 LEU cc_start: 0.9065 (tp) cc_final: 0.8838 (tp)
REVERT: A  588 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8023 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1703
  time to fit residues: 29.7112
Evaluate side-chains
  96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0070
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7000

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.122604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.098754 restraints weight = 21480.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.101891 restraints weight = 11619.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.104080 restraints weight = 7497.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6763  Z= 0.165
  Angle     :  0.756   9.946   9192  Z= 0.374
  Chirality :  0.051   0.458    968
  Planarity :  0.005   0.048   1168
  Dihedral  :  8.467  88.878   1016
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.09 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.29), residues: 786
  helix: -0.08 (0.25), residues: 393
  sheet: -0.46 (0.94), residues: 29
  loop : -1.26 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 460 
 HIS   0.003   0.001   HIS A 264 
 PHE   0.023   0.002   PHE A  28 
 TYR   0.043   0.002   TYR A 453 
 ARG   0.003   0.001   ARG A 459 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00703 (    6)
  link_NAG-ASN         : angle       3.30744 (   18)
  hydrogen bonds       : bond        0.04337 (  299)
  hydrogen bonds       : angle       5.37006 (  864)
  SS BOND              : bond        0.00338 (    5)
  SS BOND              : angle       1.19603 (   10)
  covalent geometry    : bond        0.00367 ( 6752)
  covalent geometry    : angle       0.74171 ( 9164)

*********************** 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
  130 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.756 
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: 0.7849 (mtmt) cc_final: 0.7606 (mtpt)
REVERT: B  424 LYS cc_start: 0.6956 (ttmt) cc_final: 0.6546 (tptt)
REVERT: B  499 THR cc_start: 0.8486 (p) cc_final: 0.8203 (p)
REVERT: A   62 MET cc_start: 0.8582 (ppp) cc_final: 0.8367 (ppp)
REVERT: A  151 MET cc_start: 0.6450 (tpt) cc_final: 0.6221 (tpp)
REVERT: A  164 TRP cc_start: 0.6522 (m-90) cc_final: 0.5889 (m-90)
REVERT: A  248 MET cc_start: 0.7450 (ptm) cc_final: 0.7195 (ppp)
REVERT: A  304 GLU cc_start: 0.6351 (tp30) cc_final: 0.6115 (tp30)
REVERT: A  308 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8193 (mmtm)
REVERT: A  453 TYR cc_start: 0.5639 (m-80) cc_final: 0.4964 (m-80)
REVERT: A  557 LEU cc_start: 0.9105 (mm) cc_final: 0.8863 (mm)
REVERT: A  567 LEU cc_start: 0.9062 (tp) cc_final: 0.8853 (tp)
REVERT: A  588 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8086 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1553
  time to fit residues: 27.9294
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  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 22 optimal weight:    0.1980
   chunk 53 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0370
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
B 448 ASN
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.120701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.097008 restraints weight = 20393.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.100209 restraints weight = 11212.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.102406 restraints weight = 7235.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.4345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6763  Z= 0.151
  Angle     :  0.736   9.909   9192  Z= 0.369
  Chirality :  0.050   0.495    968
  Planarity :  0.004   0.048   1168
  Dihedral  :  8.158  76.908   1016
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.96 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.02 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.29), residues: 786
  helix: -0.07 (0.25), residues: 402
  sheet: -0.38 (0.93), residues: 29
  loop : -1.18 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.003   TRP A 167 
 HIS   0.006   0.001   HIS A 525 
 PHE   0.020   0.002   PHE A 229 
 TYR   0.041   0.002   TYR A  50 
 ARG   0.007   0.001   ARG A 168 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00508 (    6)
  link_NAG-ASN         : angle       3.49220 (   18)
  hydrogen bonds       : bond        0.04198 (  299)
  hydrogen bonds       : angle       5.37604 (  864)
  SS BOND              : bond        0.00279 (    5)
  SS BOND              : angle       1.05271 (   10)
  covalent geometry    : bond        0.00337 ( 6752)
  covalent geometry    : angle       0.71981 ( 9164)

*********************** 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
  133 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.780 
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  424 LYS cc_start: 0.6962 (ttmt) cc_final: 0.6495 (tptt)
REVERT: B  499 THR cc_start: 0.8452 (p) cc_final: 0.8188 (p)
REVERT: A   30 GLU cc_start: 0.8567 (mp0) cc_final: 0.8218 (mp0)
REVERT: A  151 MET cc_start: 0.6444 (tpt) cc_final: 0.6205 (tpp)
REVERT: A  164 TRP cc_start: 0.6818 (m-90) cc_final: 0.6593 (m-90)
REVERT: A  248 MET cc_start: 0.7543 (ptm) cc_final: 0.7305 (ppp)
REVERT: A  304 GLU cc_start: 0.6472 (tp30) cc_final: 0.6234 (tp30)
REVERT: A  308 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8055 (mmtm)
REVERT: A  446 VAL cc_start: 0.8764 (m) cc_final: 0.8450 (p)
REVERT: A  453 TYR cc_start: 0.5412 (m-80) cc_final: 0.4754 (m-80)
REVERT: A  557 LEU cc_start: 0.8951 (mm) cc_final: 0.8713 (mm)
REVERT: A  588 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8078 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1708
  time to fit residues: 30.8506
Evaluate side-chains
  95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.122413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.098752 restraints weight = 21297.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.101772 restraints weight = 11569.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.103758 restraints weight = 7559.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.4655

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= 0.155
  Angle     :  0.739  10.758   9192  Z= 0.367
  Chirality :  0.050   0.405    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  7.390  56.109   1016
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 17.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.47 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.74 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.29), residues: 786
  helix: -0.09 (0.25), residues: 414
  sheet: -0.41 (0.96), residues: 29
  loop : -1.19 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 353 
 HIS   0.004   0.001   HIS A 264 
 PHE   0.025   0.002   PHE A 229 
 TYR   0.053   0.002   TYR A  50 
 ARG   0.003   0.000   ARG A 305 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00617 (    6)
  link_NAG-ASN         : angle       3.29362 (   18)
  hydrogen bonds       : bond        0.04049 (  299)
  hydrogen bonds       : angle       5.22917 (  864)
  SS BOND              : bond        0.00456 (    5)
  SS BOND              : angle       1.66247 (   10)
  covalent geometry    : bond        0.00343 ( 6752)
  covalent geometry    : angle       0.72383 ( 9164)

*********************** 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
  124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  499 THR cc_start: 0.8477 (p) cc_final: 0.8201 (p)
REVERT: A   30 GLU cc_start: 0.8592 (mp0) cc_final: 0.8342 (mp0)
REVERT: A  151 MET cc_start: 0.6420 (tpt) cc_final: 0.6167 (tpp)
REVERT: A  248 MET cc_start: 0.7492 (ptm) cc_final: 0.7284 (ppp)
REVERT: A  304 GLU cc_start: 0.6480 (tp30) cc_final: 0.6264 (tp30)
REVERT: A  308 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8173 (mmtm)
REVERT: A  326 PHE cc_start: 0.6491 (m-80) cc_final: 0.6058 (m-80)
REVERT: A  446 VAL cc_start: 0.8823 (m) cc_final: 0.8595 (p)
REVERT: A  453 TYR cc_start: 0.4969 (m-80) cc_final: 0.4358 (m-80)
REVERT: A  503 PHE cc_start: 0.8882 (t80) cc_final: 0.8637 (t80)
REVERT: A  557 LEU cc_start: 0.8946 (mm) cc_final: 0.8649 (mm)
REVERT: A  588 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8160 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1816
  time to fit residues: 31.6750
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  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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  58 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 = 0.4029 r_free = 0.4029 target = 0.118597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.095111 restraints weight = 20620.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.098270 restraints weight = 11196.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.100299 restraints weight = 7162.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6763  Z= 0.169
  Angle     :  0.767  10.260   9192  Z= 0.384
  Chirality :  0.051   0.397    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  6.879  55.032   1016
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 19.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.34 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.29), residues: 786
  helix: -0.16 (0.25), residues: 413
  sheet: -1.03 (0.86), residues: 40
  loop : -1.18 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.003   TRP A 167 
 HIS   0.002   0.001   HIS A 264 
 PHE   0.030   0.002   PHE A 229 
 TYR   0.041   0.002   TYR A 453 
 ARG   0.002   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00601 (    6)
  link_NAG-ASN         : angle       3.46649 (   18)
  hydrogen bonds       : bond        0.04173 (  299)
  hydrogen bonds       : angle       5.37199 (  864)
  SS BOND              : bond        0.00158 (    5)
  SS BOND              : angle       1.34820 (   10)
  covalent geometry    : bond        0.00376 ( 6752)
  covalent geometry    : angle       0.75113 ( 9164)

*********************** 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
  126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.781 
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  499 THR cc_start: 0.8506 (p) cc_final: 0.8233 (p)
REVERT: A  123 MET cc_start: 0.8921 (mmp) cc_final: 0.8720 (mmm)
REVERT: A  151 MET cc_start: 0.6498 (tpt) cc_final: 0.6201 (tpp)
REVERT: A  164 TRP cc_start: 0.7103 (m-90) cc_final: 0.6802 (m-90)
REVERT: A  248 MET cc_start: 0.7598 (ptm) cc_final: 0.7387 (ppp)
REVERT: A  308 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8169 (mmtm)
REVERT: A  380 TYR cc_start: 0.8465 (t80) cc_final: 0.8190 (t80)
REVERT: A  446 VAL cc_start: 0.8803 (m) cc_final: 0.8535 (p)
REVERT: A  451 PHE cc_start: 0.9004 (t80) cc_final: 0.8779 (t80)
REVERT: A  453 TYR cc_start: 0.5200 (m-80) cc_final: 0.4378 (m-80)
REVERT: A  455 LEU cc_start: 0.9348 (mt) cc_final: 0.8997 (mt)
REVERT: A  557 LEU cc_start: 0.9055 (mm) cc_final: 0.8594 (mm)
REVERT: A  588 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8171 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1734
  time to fit residues: 29.7605
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  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0980
   chunk 60 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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  58 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 = 0.4033 r_free = 0.4033 target = 0.118944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.095124 restraints weight = 20848.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.098257 restraints weight = 11415.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.100407 restraints weight = 7366.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.5062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6763  Z= 0.161
  Angle     :  0.785  19.107   9192  Z= 0.389
  Chirality :  0.051   0.386    968
  Planarity :  0.004   0.047   1168
  Dihedral  :  6.576  56.732   1016
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 19.02
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.34 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.29), residues: 786
  helix: -0.05 (0.25), residues: 402
  sheet: -1.00 (0.86), residues: 40
  loop : -1.19 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.003   TRP A 167 
 HIS   0.006   0.001   HIS A 525 
 PHE   0.027   0.002   PHE A 229 
 TYR   0.054   0.002   TYR A  50 
 ARG   0.003   0.000   ARG A 459 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00558 (    6)
  link_NAG-ASN         : angle       3.24586 (   18)
  hydrogen bonds       : bond        0.04105 (  299)
  hydrogen bonds       : angle       5.32727 (  864)
  SS BOND              : bond        0.00330 (    5)
  SS BOND              : angle       1.29123 (   10)
  covalent geometry    : bond        0.00367 ( 6752)
  covalent geometry    : angle       0.77133 ( 9164)

*********************** 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
  129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.773 
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: B  499 THR cc_start: 0.8406 (p) cc_final: 0.8165 (p)
REVERT: A  151 MET cc_start: 0.6469 (tpt) cc_final: 0.6211 (tpp)
REVERT: A  164 TRP cc_start: 0.6959 (m-90) cc_final: 0.6505 (m-90)
REVERT: A  304 GLU cc_start: 0.6581 (tp30) cc_final: 0.6347 (tp30)
REVERT: A  308 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8279 (mmtm)
REVERT: A  322 MET cc_start: 0.7284 (tpt) cc_final: 0.6784 (tpt)
REVERT: A  407 MET cc_start: 0.9218 (mmm) cc_final: 0.8882 (mmt)
REVERT: A  453 TYR cc_start: 0.4895 (m-80) cc_final: 0.4387 (m-80)
REVERT: A  455 LEU cc_start: 0.9358 (mt) cc_final: 0.9003 (mt)
REVERT: A  525 HIS cc_start: 0.8116 (t70) cc_final: 0.7906 (t-90)
REVERT: A  588 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8178 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1808
  time to fit residues: 31.9590
Evaluate side-chains
  94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0030
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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 477 ASN
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.118778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.095283 restraints weight = 20790.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.098510 restraints weight = 11200.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.100717 restraints weight = 7127.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.5259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6763  Z= 0.163
  Angle     :  0.761  10.152   9192  Z= 0.382
  Chirality :  0.051   0.388    968
  Planarity :  0.005   0.056   1168
  Dihedral  :  6.457  56.894   1016
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 18.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.47 %
    Favored  : 94.40 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.30), residues: 786
  helix: -0.07 (0.25), residues: 402
  sheet: -0.79 (0.85), residues: 39
  loop : -1.16 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.004   TRP A 167 
 HIS   0.006   0.001   HIS A 525 
 PHE   0.030   0.002   PHE A 229 
 TYR   0.049   0.002   TYR A  50 
 ARG   0.009   0.001   ARG A 305 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00578 (    6)
  link_NAG-ASN         : angle       3.12214 (   18)
  hydrogen bonds       : bond        0.04255 (  299)
  hydrogen bonds       : angle       5.43027 (  864)
  SS BOND              : bond        0.00275 (    5)
  SS BOND              : angle       1.32962 (   10)
  covalent geometry    : bond        0.00376 ( 6752)
  covalent geometry    : angle       0.74789 ( 9164)

********************** 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
  126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.763 
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  499 THR cc_start: 0.8402 (p) cc_final: 0.8127 (p)
REVERT: A  164 TRP cc_start: 0.6677 (m-90) cc_final: 0.6476 (m-90)
REVERT: A  407 MET cc_start: 0.9206 (mmm) cc_final: 0.8871 (mmt)
REVERT: A  451 PHE cc_start: 0.9107 (t80) cc_final: 0.8860 (t80)
REVERT: A  453 TYR cc_start: 0.4772 (m-80) cc_final: 0.4414 (m-80)
REVERT: A  455 LEU cc_start: 0.9491 (mt) cc_final: 0.9257 (mt)
REVERT: A  588 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8167 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1811
  time to fit residues: 31.1211
Evaluate side-chains
  92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 49 optimal weight:    0.4980
   chunk 75 optimal weight:    0.1980
   chunk 19 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    0.4980
   chunk 65 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 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 = 0.4046 r_free = 0.4046 target = 0.119689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.096595 restraints weight = 20338.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.099833 restraints weight = 10955.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.102001 restraints weight = 6943.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.5410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6763  Z= 0.153
  Angle     :  0.765  10.063   9192  Z= 0.383
  Chirality :  0.051   0.385    968
  Planarity :  0.005   0.048   1168
  Dihedral  :  6.336  56.353   1016
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 18.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.47 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.30), residues: 786
  helix: -0.11 (0.25), residues: 402
  sheet: -0.85 (0.85), residues: 40
  loop : -1.18 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.003   TRP A 167 
 HIS   0.005   0.001   HIS A 525 
 PHE   0.025   0.002   PHE A 229 
 TYR   0.046   0.002   TYR A  50 
 ARG   0.008   0.001   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00572 (    6)
  link_NAG-ASN         : angle       2.98873 (   18)
  hydrogen bonds       : bond        0.04159 (  299)
  hydrogen bonds       : angle       5.40464 (  864)
  SS BOND              : bond        0.00263 (    5)
  SS BOND              : angle       1.23318 (   10)
  covalent geometry    : bond        0.00345 ( 6752)
  covalent geometry    : angle       0.75334 ( 9164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2524.64 seconds
wall clock time: 45 minutes 19.97 seconds (2719.97 seconds total)