Starting phenix.real_space_refine
on Thu Jul 24 20:49:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dv2_27731/07_2025/8dv2_27731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dv2_27731/07_2025/8dv2_27731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2025/8dv2_27731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2025/8dv2_27731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2025/8dv2_27731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2025/8dv2_27731.cif"
  }
  resolution = 3.5
  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=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4186      2.51       5
     N    1075      2.21       5
     O    1247      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6545
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1590
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "D"
      Number of atoms: 4857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4857
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 11.58, per 1000 atoms: 1.77
  Number of scatterers: 6545
  At special positions: 0
  Unit cell: (76.608, 88.704, 122.976, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1247      8.00
     N    1075      7.00
     C    4186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.06
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " 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 A1301 " - " ASN A 343 "
      " NAG D1101 " - " ASN D 322 "
      " NAG D1102 " - " ASN D 103 "
      " NAG D1103 " - " ASN D 432 "
      " NAG D1104 " - " ASN D 546 "
      " NAG D1105 " - " ASN D  90 "
      " NAG D1106 " - " ASN D  53 "
  Time building additional restraints: 3.32
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1498

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 7 sheets defined
      57.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.623A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 386 through 389
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.367A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
      removed outlier: 3.645A  pdb=" N   TYR A 421 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'D' and resid 22 through 53
      removed outlier: 4.268A  pdb=" N   ASP D  38 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 80
    Processing helix  chain 'D' and resid 81 through 83
      No H-bonds generated for 'chain 'D' and resid 81 through 83'
    Processing helix  chain 'D' and resid 84 through 88
    Processing helix  chain 'D' and resid 90 through 101
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 147 through 155
    Processing helix  chain 'D' and resid 157 through 170
      removed outlier: 3.605A  pdb=" N   TRP D 168 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG D 169 " --> pdb=" O   TRP D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 194
      Proline residue:  D 178  - end of helix
      removed outlier: 3.790A  pdb=" N   GLU D 182 " --> pdb=" O   PRO D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 219 through 249
      removed outlier: 4.248A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 277
      No H-bonds generated for 'chain 'D' and resid 275 through 277'
    Processing helix  chain 'D' and resid 278 through 283
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 303 through 318
    Processing helix  chain 'D' and resid 324 through 331
    Processing helix  chain 'D' and resid 365 through 385
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 414
      removed outlier: 3.685A  pdb=" N   THR D 414 " --> pdb=" O   LEU D 410 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
    Processing helix  chain 'D' and resid 449 through 465
    Processing helix  chain 'D' and resid 472 through 484
    Processing helix  chain 'D' and resid 498 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 4.107A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
    Processing helix  chain 'D' and resid 581 through 599
      Proline residue:  D 590  - end of helix
      removed outlier: 3.617A  pdb=" N   ASP D 597 " --> pdb=" O   THR D 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 600 through 602
      No H-bonds generated for 'chain 'D' and resid 600 through 602'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.709A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 133
    Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 263
      removed outlier: 6.082A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 350

    322 hydrogen bonds defined for protein.
    909 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: 3.23

  Time building geometry restraints manager: 3.46 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1305
        1.32 -     1.45: 2125
        1.45 -     1.58: 3229
        1.58 -     1.71: 10
        1.71 -     1.84: 58
  Bond restraints: 6727
  Sorted by residual:
  bond pdb=" CB  HIS D 265 "
       pdb=" CG  HIS D 265 "
    ideal  model  delta    sigma   weight residual
    1.497  1.425  0.072 1.40e-02 5.10e+03 2.68e+01
  bond pdb=" CB  HIS D 535 "
       pdb=" CG  HIS D 535 "
    ideal  model  delta    sigma   weight residual
    1.497  1.425  0.072 1.40e-02 5.10e+03 2.64e+01
  bond pdb=" CB  ASN A 422 "
       pdb=" CG  ASN A 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.391  0.125 2.50e-02 1.60e+03 2.50e+01
  bond pdb=" CZ  ARG D 460 "
       pdb=" NH2 ARG D 460 "
    ideal  model  delta    sigma   weight residual
    1.330  1.274  0.056 1.30e-02 5.92e+03 1.83e+01
  bond pdb=" CZ  ARG D 161 "
       pdb=" NH2 ARG D 161 "
    ideal  model  delta    sigma   weight residual
    1.330  1.278  0.052 1.30e-02 5.92e+03 1.60e+01
  ... (remaining 6722 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 7882
        2.33 -     4.67: 1070
        4.67 -     7.00: 171
        7.00 -     9.33: 15
        9.33 -    11.67: 5
  Bond angle restraints: 9143
  Sorted by residual:
  angle pdb=" N   SER D 170 "
        pdb=" CA  SER D 170 "
        pdb=" C   SER D 170 "
      ideal   model   delta    sigma   weight residual
     110.35   98.98   11.37 1.38e+00 5.25e-01 6.79e+01
  angle pdb=" C   GLU D 489 "
        pdb=" N   PRO D 490 "
        pdb=" CA  PRO D 490 "
      ideal   model   delta    sigma   weight residual
     119.87  128.34   -8.47 1.04e+00 9.25e-01 6.63e+01
  angle pdb=" C   GLY A 526 "
        pdb=" N   PRO A 527 "
        pdb=" CA  PRO A 527 "
      ideal   model   delta    sigma   weight residual
     119.85  127.88   -8.03 1.01e+00 9.80e-01 6.33e+01
  angle pdb=" CB  ASN D  90 "
        pdb=" CG  ASN D  90 "
        pdb=" ND2 ASN D  90 "
      ideal   model   delta    sigma   weight residual
     116.40  128.07  -11.67 1.50e+00 4.44e-01 6.05e+01
  angle pdb=" N   TYR A 380 "
        pdb=" CA  TYR A 380 "
        pdb=" C   TYR A 380 "
      ideal   model   delta    sigma   weight residual
     114.31  104.49    9.82 1.29e+00 6.01e-01 5.80e+01
  ... (remaining 9138 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 3878
       17.29 -    34.58: 140
       34.58 -    51.88: 25
       51.88 -    69.17: 15
       69.17 -    86.46: 5
  Dihedral angle restraints: 4063
    sinusoidal: 1728
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" C   TYR A 421 "
           pdb=" N   TYR A 421 "
           pdb=" CA  TYR A 421 "
           pdb=" CB  TYR A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.06   11.46     0      2.50e+00 1.60e-01 2.10e+01
  dihedral pdb=" N   TYR A 421 "
           pdb=" C   TYR A 421 "
           pdb=" CA  TYR A 421 "
           pdb=" CB  TYR A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.46  -10.66     0      2.50e+00 1.60e-01 1.82e+01
  dihedral pdb=" CA  PRO D 389 "
           pdb=" C   PRO D 389 "
           pdb=" N   PHE D 390 "
           pdb=" CA  PHE D 390 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 4060 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.114: 739
       0.114 -    0.229: 209
       0.229 -    0.343: 21
       0.343 -    0.457: 7
       0.457 -    0.572: 1
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CA  TYR A 421 "
            pdb=" N   TYR A 421 "
            pdb=" C   TYR A 421 "
            pdb=" CB  TYR A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.17e+00
  chirality pdb=" C1  NAG D1102 "
            pdb=" ND2 ASN D 103 "
            pdb=" C2  NAG D1102 "
            pdb=" O5  NAG D1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.84    0.44 2.00e-01 2.50e+01 4.84e+00
  chirality pdb=" C1  NAG D1104 "
            pdb=" ND2 ASN D 546 "
            pdb=" C2  NAG D1104 "
            pdb=" O5  NAG D1104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.79    0.39 2.00e-01 2.50e+01 3.83e+00
  ... (remaining 974 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  53 "    0.015 2.00e-02 2.50e+03   7.67e-02 7.35e+01
        pdb=" CG  ASN D  53 "    0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  53 "   -0.076 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  53 "    0.125 2.00e-02 2.50e+03
        pdb=" C1  NAG D1106 "   -0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 103 "   -0.013 2.00e-02 2.50e+03   4.66e-02 2.71e+01
        pdb=" CG  ASN D 103 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 103 "    0.046 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 103 "   -0.075 2.00e-02 2.50e+03
        pdb=" C1  NAG D1102 "    0.053 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 432 "   -0.008 2.00e-02 2.50e+03   4.30e-02 2.31e+01
        pdb=" CG  ASN D 432 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 432 "    0.043 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 432 "   -0.069 2.00e-02 2.50e+03
        pdb=" C1  NAG D1103 "    0.048 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1264
        2.76 -     3.29: 6404
        3.29 -     3.83: 11299
        3.83 -     4.36: 14413
        4.36 -     4.90: 22737
  Nonbonded interactions: 56117
  Sorted by model distance:
  nonbonded pdb=" O4  NAG D1102 "
            pdb=" O6  NAG D1102 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O4  NAG D1101 "
            pdb=" O6  NAG D1101 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" N   SER D 170 "
            pdb=" O   SER D 170 "
     model   vdw
     2.348 2.496
  nonbonded pdb=" O4  NAG D1104 "
            pdb=" O6  NAG D1104 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" N   TYR A 380 "
            pdb=" N   GLY A 381 "
     model   vdw
     2.385 2.560
  ... (remaining 56112 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:             654.430
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     36.210
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.080
  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:4.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  695.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
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      :  0.018   0.135   6741  Z= 0.965
  Angle     :  1.707  12.716   9178  Z= 1.149
  Chirality :  0.104   0.572    977
  Planarity :  0.009   0.067   1177
  Dihedral  : 10.740  86.458   2544
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.89 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.00 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.17 (0.28), residues: 792
  helix: -0.42 (0.23), residues: 391
  sheet:  0.78 (0.73), residues: 61
  loop :  0.38 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.009   TRP D 349 
 HIS   0.014   0.003   HIS D 535 
 PHE   0.028   0.006   PHE D 390 
 TYR   0.059   0.008   TYR D 199 
 ARG   0.010   0.001   ARG D 161 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.10760 (    7)
  link_NAG-ASN         : angle       6.52173 (   21)
  hydrogen bonds       : bond        0.17310 (  322)
  hydrogen bonds       : angle       7.10652 (  909)
  SS BOND              : bond        0.01568 (    7)
  SS BOND              : angle       2.49216 (   14)
  covalent geometry    : bond        0.01778 ( 6727)
  covalent geometry    : angle       1.67848 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ASN cc_start: 0.7073 (t0) cc_final: 0.6510 (m110)
REVERT: A  418 ILE cc_start: 0.9251 (mm) cc_final: 0.8602 (mm)
REVERT: D  119 ILE cc_start: 0.8518 (mt) cc_final: 0.8257 (mt)
REVERT: D  155 SER cc_start: 0.8440 (t) cc_final: 0.8027 (p)
REVERT: D  291 ILE cc_start: 0.8495 (pt) cc_final: 0.7995 (mp)
REVERT: D  362 THR cc_start: 0.7357 (m) cc_final: 0.6892 (m)
REVERT: D  441 LYS cc_start: 0.8693 (tttt) cc_final: 0.8471 (tptp)
REVERT: D  474 MET cc_start: 0.8360 (mmp) cc_final: 0.8030 (mmm)
REVERT: D  480 MET cc_start: 0.8661 (mtp) cc_final: 0.8432 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 207
  average time/residue: 0.3169
  time to fit residues: 84.3893
Evaluate side-chains
  117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.0170
   chunk 59 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 46 optimal weight:    0.1980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.4018

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
A 493 GLN
A 498 GLN
A 506 GLN
D 154 ASN
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.096670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.085626 restraints weight = 18050.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.088263 restraints weight = 8189.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.089974 restraints weight = 4711.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6741  Z= 0.159
  Angle     :  0.829  20.748   9178  Z= 0.389
  Chirality :  0.056   0.767    977
  Planarity :  0.005   0.055   1177
  Dihedral  :  8.090  88.017   1013
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.89 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.01 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.96 (0.30), residues: 792
  helix:  1.11 (0.26), residues: 390
  sheet:  0.06 (0.72), residues: 61
  loop :  0.36 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 374 
 PHE   0.017   0.001   PHE D 369 
 TYR   0.017   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01613 (    7)
  link_NAG-ASN         : angle       9.24395 (   21)
  hydrogen bonds       : bond        0.05638 (  322)
  hydrogen bonds       : angle       5.31924 (  909)
  SS BOND              : bond        0.00587 (    7)
  SS BOND              : angle       0.93410 (   14)
  covalent geometry    : bond        0.00320 ( 6727)
  covalent geometry    : angle       0.70205 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  206 ASP cc_start: 0.8612 (t0) cc_final: 0.8285 (t0)
REVERT: D  441 LYS cc_start: 0.8817 (tttt) cc_final: 0.8354 (tptp)
REVERT: D  483 GLU cc_start: 0.8445 (tp30) cc_final: 0.8013 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 158
  average time/residue: 0.2653
  time to fit residues: 55.8599
Evaluate side-chains
  108 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  379 ILE
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  503 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 47 optimal weight:    0.3980
   chunk 65 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   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 493 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 373 HIS
D 401 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.094416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.083689 restraints weight = 18172.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.086068 restraints weight = 8576.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.087564 restraints weight = 5070.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.4106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6741  Z= 0.156
  Angle     :  0.773  20.944   9178  Z= 0.364
  Chirality :  0.053   0.587    977
  Planarity :  0.004   0.050   1177
  Dihedral  :  7.720  86.124   1013
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.02 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.59 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.12 (0.30), residues: 792
  helix:  1.32 (0.26), residues: 393
  sheet: -0.03 (0.69), residues: 60
  loop :  0.36 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D 478 
 HIS   0.004   0.001   HIS D 535 
 PHE   0.024   0.002   PHE D 327 
 TYR   0.022   0.001   TYR A 380 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01310 (    7)
  link_NAG-ASN         : angle       8.27248 (   21)
  hydrogen bonds       : bond        0.05193 (  322)
  hydrogen bonds       : angle       5.04890 (  909)
  SS BOND              : bond        0.00687 (    7)
  SS BOND              : angle       1.95926 (   14)
  covalent geometry    : bond        0.00331 ( 6727)
  covalent geometry    : angle       0.66101 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 1.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7493 (t0) cc_final: 0.7267 (t0)
REVERT: A  462 LYS cc_start: 0.7735 (mppt) cc_final: 0.7380 (mppt)
REVERT: D   74 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8851 (mtmm)
REVERT: D  206 ASP cc_start: 0.8547 (t0) cc_final: 0.7894 (t0)
REVERT: D  285 PHE cc_start: 0.6834 (m-80) cc_final: 0.6096 (m-80)
REVERT: D  287 GLN cc_start: 0.5950 (pm20) cc_final: 0.5378 (mm-40)
REVERT: D  360 MET cc_start: 0.7963 (tmm) cc_final: 0.7511 (ttt)
REVERT: D  406 GLU cc_start: 0.8393 (tp30) cc_final: 0.7726 (tp30)
REVERT: D  441 LYS cc_start: 0.8844 (tttt) cc_final: 0.8405 (tptp)
REVERT: D  470 LYS cc_start: 0.7688 (mmmm) cc_final: 0.7091 (mmmm)
REVERT: D  483 GLU cc_start: 0.8406 (tp30) cc_final: 0.8110 (tp30)
REVERT: D  601 ASN cc_start: 0.8057 (t0) cc_final: 0.7809 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 129
  average time/residue: 0.3095
  time to fit residues: 53.5679
Evaluate side-chains
  118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0670
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0980
   overall best weight:    0.5720

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN
D 210 ASN
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 401 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.093751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.082880 restraints weight = 18554.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.085273 restraints weight = 8783.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.086847 restraints weight = 5185.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6741  Z= 0.146
  Angle     :  0.732  21.010   9178  Z= 0.341
  Chirality :  0.051   0.486    977
  Planarity :  0.004   0.050   1177
  Dihedral  :  6.814  64.178   1013
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.02 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.02 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.09 (0.30), residues: 792
  helix:  1.39 (0.26), residues: 401
  sheet: -0.16 (0.69), residues: 60
  loop :  0.21 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 478 
 HIS   0.003   0.001   HIS D 535 
 PHE   0.025   0.001   PHE D 327 
 TYR   0.019   0.001   TYR D 497 
 ARG   0.002   0.000   ARG A 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01182 (    7)
  link_NAG-ASN         : angle       8.01947 (   21)
  hydrogen bonds       : bond        0.04708 (  322)
  hydrogen bonds       : angle       4.79114 (  909)
  SS BOND              : bond        0.00595 (    7)
  SS BOND              : angle       1.57073 (   14)
  covalent geometry    : bond        0.00317 ( 6727)
  covalent geometry    : angle       0.62219 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7238 (t0) cc_final: 0.6950 (t0)
REVERT: D  152 MET cc_start: 0.6273 (mmm) cc_final: 0.6047 (mmm)
REVERT: D  270 MET cc_start: 0.7696 (tpp) cc_final: 0.7299 (tpp)
REVERT: D  360 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7594 (ttt)
REVERT: D  375 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7995 (mm-30)
REVERT: D  406 GLU cc_start: 0.8332 (tp30) cc_final: 0.7614 (tp30)
REVERT: D  435 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7338 (mt-10)
REVERT: D  441 LYS cc_start: 0.8819 (tttt) cc_final: 0.8404 (tptp)
REVERT: D  470 LYS cc_start: 0.8093 (mmmm) cc_final: 0.7741 (mmtt)
REVERT: D  483 GLU cc_start: 0.8450 (tp30) cc_final: 0.8185 (tp30)
REVERT: D  488 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7685 (m)
REVERT: D  601 ASN cc_start: 0.8107 (t0) cc_final: 0.7895 (t0)
  outliers start: 20
  outliers final: 15
  residues processed: 126
  average time/residue: 0.4034
  time to fit residues: 70.8479
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 1.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  360 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  487 VAL
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 73 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 77 optimal weight:    0.2980
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 38 optimal weight:    0.4980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 417 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.093289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.082509 restraints weight = 18440.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.084835 restraints weight = 8806.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.086356 restraints weight = 5270.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.5066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   6741  Z= 0.145
  Angle     :  0.713  21.040   9178  Z= 0.334
  Chirality :  0.050   0.439    977
  Planarity :  0.004   0.049   1177
  Dihedral  :  5.926  52.378   1013
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.78 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 13.45 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.25 (0.30), residues: 792
  helix:  1.57 (0.26), residues: 397
  sheet: -0.21 (0.70), residues: 60
  loop :  0.25 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 535 
 PHE   0.025   0.002   PHE D 327 
 TYR   0.023   0.001   TYR D 497 
 ARG   0.002   0.000   ARG A 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01176 (    7)
  link_NAG-ASN         : angle       8.04027 (   21)
  hydrogen bonds       : bond        0.04535 (  322)
  hydrogen bonds       : angle       4.70063 (  909)
  SS BOND              : bond        0.00507 (    7)
  SS BOND              : angle       1.25841 (   14)
  covalent geometry    : bond        0.00323 ( 6727)
  covalent geometry    : angle       0.59964 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 1.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7242 (t0) cc_final: 0.6998 (t0)
REVERT: A  417 LYS cc_start: 0.9173 (tppt) cc_final: 0.8668 (tppt)
REVERT: A  421 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6148 (p90)
REVERT: A  462 LYS cc_start: 0.7907 (mppt) cc_final: 0.7557 (mppt)
REVERT: D  152 MET cc_start: 0.6348 (mmm) cc_final: 0.6141 (mmm)
REVERT: D  270 MET cc_start: 0.7753 (tpp) cc_final: 0.7543 (tpp)
REVERT: D  323 MET cc_start: 0.9402 (tpp) cc_final: 0.9090 (mmm)
REVERT: D  360 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6998 (tmm)
REVERT: D  375 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7930 (mm-30)
REVERT: D  406 GLU cc_start: 0.8327 (tp30) cc_final: 0.7661 (tp30)
REVERT: D  441 LYS cc_start: 0.8809 (tttt) cc_final: 0.8432 (tptp)
REVERT: D  483 GLU cc_start: 0.8516 (tp30) cc_final: 0.8267 (tp30)
REVERT: D  488 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7833 (m)
REVERT: D  493 HIS cc_start: 0.6499 (m-70) cc_final: 0.5574 (m90)
  outliers start: 24
  outliers final: 16
  residues processed: 127
  average time/residue: 0.2970
  time to fit residues: 50.6310
Evaluate side-chains
  118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 1.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  360 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  487 VAL
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 HIS ** 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 = 0.3493 r_free = 0.3493 target = 0.091448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.080847 restraints weight = 18510.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.083130 restraints weight = 8863.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.084638 restraints weight = 5317.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.5378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6741  Z= 0.178
  Angle     :  0.732  21.135   9178  Z= 0.348
  Chirality :  0.051   0.432    977
  Planarity :  0.004   0.046   1177
  Dihedral  :  5.836  53.174   1013
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.78 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 14.02 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.26 (0.30), residues: 792
  helix:  1.62 (0.26), residues: 396
  sheet: -0.30 (0.70), residues: 60
  loop :  0.23 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D 478 
 HIS   0.005   0.001   HIS D 493 
 PHE   0.024   0.002   PHE D 327 
 TYR   0.021   0.002   TYR D 497 
 ARG   0.003   0.001   ARG A 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01117 (    7)
  link_NAG-ASN         : angle       8.06546 (   21)
  hydrogen bonds       : bond        0.04766 (  322)
  hydrogen bonds       : angle       4.72820 (  909)
  SS BOND              : bond        0.00561 (    7)
  SS BOND              : angle       1.29649 (   14)
  covalent geometry    : bond        0.00395 ( 6727)
  covalent geometry    : angle       0.62110 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7260 (t0) cc_final: 0.7045 (t0)
REVERT: A  462 LYS cc_start: 0.7946 (mppt) cc_final: 0.7584 (mppt)
REVERT: D  115 ARG cc_start: 0.8542 (tpp-160) cc_final: 0.8288 (tpm170)
REVERT: D  152 MET cc_start: 0.6609 (mmm) cc_final: 0.6286 (mmm)
REVERT: D  270 MET cc_start: 0.7804 (tpp) cc_final: 0.7504 (tpp)
REVERT: D  323 MET cc_start: 0.9405 (tpp) cc_final: 0.9141 (mmm)
REVERT: D  366 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8070 (ttp)
REVERT: D  375 GLU cc_start: 0.8728 (mm-30) cc_final: 0.7988 (mm-30)
REVERT: D  406 GLU cc_start: 0.8344 (tp30) cc_final: 0.7776 (tp30)
REVERT: D  441 LYS cc_start: 0.8836 (tttt) cc_final: 0.8443 (tptp)
REVERT: D  488 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7976 (m)
REVERT: D  493 HIS cc_start: 0.6454 (m-70) cc_final: 0.5398 (m-70)
REVERT: D  589 GLU cc_start: 0.7779 (tp30) cc_final: 0.7575 (tp30)
  outliers start: 27
  outliers final: 22
  residues processed: 112
  average time/residue: 0.3612
  time to fit residues: 54.2854
Evaluate side-chains
  118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  261 CYS
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  333 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  487 VAL
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 47 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 32 optimal weight:    0.2980
   chunk 64 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0870
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 75 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** 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 = 0.3544 r_free = 0.3544 target = 0.094382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.083537 restraints weight = 18591.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.085892 restraints weight = 8993.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.087453 restraints weight = 5406.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.5620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6741  Z= 0.124
  Angle     :  0.680  21.055   9178  Z= 0.318
  Chirality :  0.048   0.404    977
  Planarity :  0.004   0.047   1177
  Dihedral  :  5.508  52.009   1013
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.40 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.31 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.54 (0.31), residues: 792
  helix:  1.80 (0.26), residues: 394
  sheet:  0.23 (0.78), residues: 50
  loop :  0.35 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP D 478 
 HIS   0.002   0.001   HIS D 493 
 PHE   0.017   0.001   PHE D  31 
 TYR   0.017   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 115 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01199 (    7)
  link_NAG-ASN         : angle       7.76264 (   21)
  hydrogen bonds       : bond        0.04196 (  322)
  hydrogen bonds       : angle       4.58898 (  909)
  SS BOND              : bond        0.00450 (    7)
  SS BOND              : angle       1.07373 (   14)
  covalent geometry    : bond        0.00273 ( 6727)
  covalent geometry    : angle       0.56971 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LYS cc_start: 0.7895 (mppt) cc_final: 0.7476 (mppt)
REVERT: D  152 MET cc_start: 0.6503 (mmm) cc_final: 0.6223 (mmm)
REVERT: D  375 GLU cc_start: 0.8659 (mm-30) cc_final: 0.7952 (mm-30)
REVERT: D  441 LYS cc_start: 0.8778 (tttt) cc_final: 0.8303 (tptp)
REVERT: D  493 HIS cc_start: 0.6675 (m-70) cc_final: 0.6060 (m-70)
REVERT: D  497 TYR cc_start: 0.7296 (m-80) cc_final: 0.6613 (m-10)
  outliers start: 22
  outliers final: 18
  residues processed: 126
  average time/residue: 0.2380
  time to fit residues: 40.3142
Evaluate side-chains
  120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  333 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 378 HIS
** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.089094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.078510 restraints weight = 18746.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.080728 restraints weight = 9087.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.082169 restraints weight = 5485.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.5788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   6741  Z= 0.249
  Angle     :  0.806  21.313   9178  Z= 0.391
  Chirality :  0.054   0.445    977
  Planarity :  0.005   0.043   1177
  Dihedral  :  6.157  54.601   1013
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.66 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.02 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.13 (0.31), residues: 792
  helix:  1.57 (0.26), residues: 397
  sheet: -0.43 (0.72), residues: 60
  loop :  0.10 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D 478 
 HIS   0.005   0.001   HIS D 493 
 PHE   0.030   0.002   PHE D 327 
 TYR   0.025   0.002   TYR D 497 
 ARG   0.004   0.001   ARG D 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01047 (    7)
  link_NAG-ASN         : angle       8.10723 (   21)
  hydrogen bonds       : bond        0.05235 (  322)
  hydrogen bonds       : angle       4.91070 (  909)
  SS BOND              : bond        0.00580 (    7)
  SS BOND              : angle       1.40547 (   14)
  covalent geometry    : bond        0.00555 ( 6727)
  covalent geometry    : angle       0.70559 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.6598 (mmm) cc_final: 0.6184 (mmm)
REVERT: D  270 MET cc_start: 0.7965 (tpp) cc_final: 0.7684 (tpp)
REVERT: D  332 MET cc_start: 0.8230 (mmm) cc_final: 0.8009 (tpp)
REVERT: D  375 GLU cc_start: 0.8659 (mm-30) cc_final: 0.7943 (mm-30)
REVERT: D  406 GLU cc_start: 0.8283 (tp30) cc_final: 0.7716 (tp30)
REVERT: D  441 LYS cc_start: 0.8851 (tttt) cc_final: 0.8479 (tptp)
REVERT: D  493 HIS cc_start: 0.6915 (m-70) cc_final: 0.6256 (m-70)
  outliers start: 24
  outliers final: 21
  residues processed: 115
  average time/residue: 0.1958
  time to fit residues: 30.0522
Evaluate side-chains
  117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  261 CYS
Chi-restraints excluded: chain D residue  333 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  487 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0050
   chunk 42 optimal weight:    2.9990
   chunk 3 optimal weight:    0.1980
   chunk 75 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 HIS ** 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 = 0.3506 r_free = 0.3506 target = 0.092139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.081368 restraints weight = 18898.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.083690 restraints weight = 9083.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.085206 restraints weight = 5454.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.5919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6741  Z= 0.143
  Angle     :  0.739  21.268   9178  Z= 0.353
  Chirality :  0.050   0.413    977
  Planarity :  0.004   0.045   1177
  Dihedral  :  5.666  52.193   1013
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.65 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.88 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.31), residues: 792
  helix:  1.71 (0.27), residues: 394
  sheet: -0.38 (0.72), residues: 60
  loop :  0.20 (0.36), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP D 478 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.028   0.002   PHE D 327 
 TYR   0.025   0.002   TYR D 158 
 ARG   0.004   0.000   ARG D 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01155 (    7)
  link_NAG-ASN         : angle       7.87498 (   21)
  hydrogen bonds       : bond        0.04528 (  322)
  hydrogen bonds       : angle       4.73841 (  909)
  SS BOND              : bond        0.00498 (    7)
  SS BOND              : angle       1.08716 (   14)
  covalent geometry    : bond        0.00319 ( 6727)
  covalent geometry    : angle       0.63597 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.6380 (mmm) cc_final: 0.6041 (mmm)
REVERT: D  249 MET cc_start: 0.6821 (mmm) cc_final: 0.6592 (mmm)
REVERT: D  270 MET cc_start: 0.8077 (tpp) cc_final: 0.7794 (tpp)
REVERT: D  323 MET cc_start: 0.9446 (tpp) cc_final: 0.9180 (mmm)
REVERT: D  332 MET cc_start: 0.8202 (mmm) cc_final: 0.7989 (tpp)
REVERT: D  406 GLU cc_start: 0.8210 (tp30) cc_final: 0.7635 (tp30)
REVERT: D  441 LYS cc_start: 0.8809 (tttt) cc_final: 0.8304 (tptp)
REVERT: D  493 HIS cc_start: 0.6861 (m-70) cc_final: 0.5610 (m-70)
  outliers start: 22
  outliers final: 17
  residues processed: 112
  average time/residue: 0.1853
  time to fit residues: 27.9734
Evaluate side-chains
  109 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  111 ASP
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  333 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 56 optimal weight:    0.0980
   chunk 26 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 71 optimal weight:    0.2980
   chunk 36 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.093914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.083266 restraints weight = 18851.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.085515 restraints weight = 9314.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.087019 restraints weight = 5691.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.6076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6741  Z= 0.140
  Angle     :  0.732  21.157   9178  Z= 0.351
  Chirality :  0.049   0.400    977
  Planarity :  0.005   0.044   1177
  Dihedral  :  5.548  52.264   1013
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.28 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.74 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.31), residues: 792
  helix:  1.70 (0.27), residues: 397
  sheet:  0.37 (0.80), residues: 50
  loop :  0.04 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 473 
 HIS   0.002   0.001   HIS D 535 
 PHE   0.028   0.002   PHE D 327 
 TYR   0.025   0.002   TYR D 158 
 ARG   0.004   0.000   ARG D 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01121 (    7)
  link_NAG-ASN         : angle       7.67779 (   21)
  hydrogen bonds       : bond        0.04356 (  322)
  hydrogen bonds       : angle       4.66111 (  909)
  SS BOND              : bond        0.00483 (    7)
  SS BOND              : angle       1.08066 (   14)
  covalent geometry    : bond        0.00313 ( 6727)
  covalent geometry    : angle       0.63294 ( 9143)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.6397 (mmm) cc_final: 0.6095 (mmt)
REVERT: D  249 MET cc_start: 0.6869 (mmm) cc_final: 0.6621 (mmm)
REVERT: D  270 MET cc_start: 0.8136 (tpp) cc_final: 0.7855 (tpp)
REVERT: D  323 MET cc_start: 0.9431 (tpp) cc_final: 0.9131 (mmm)
REVERT: D  375 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7909 (mm-30)
REVERT: D  406 GLU cc_start: 0.8147 (tp30) cc_final: 0.7601 (tp30)
REVERT: D  441 LYS cc_start: 0.8769 (tttt) cc_final: 0.8295 (tptp)
REVERT: D  474 MET cc_start: 0.8292 (mmp) cc_final: 0.8066 (mmm)
REVERT: D  479 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8218 (tm-30)
REVERT: D  493 HIS cc_start: 0.6744 (m-70) cc_final: 0.5697 (m-70)
  outliers start: 18
  outliers final: 16
  residues processed: 109
  average time/residue: 0.1844
  time to fit residues: 27.1837
Evaluate side-chains
  113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  111 ASP
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  333 LEU
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 HIS ** 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 = 0.3503 r_free = 0.3503 target = 0.092039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.081360 restraints weight = 19105.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.083587 restraints weight = 9535.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.085055 restraints weight = 5848.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.6141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6741  Z= 0.179
  Angle     :  0.764  21.166   9178  Z= 0.367
  Chirality :  0.050   0.412    977
  Planarity :  0.005   0.052   1177
  Dihedral  :  5.726  53.117   1013
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.54 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.17 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.13 (0.31), residues: 792
  helix:  1.59 (0.27), residues: 397
  sheet: -0.24 (0.74), residues: 60
  loop :  0.03 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP D 478 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.030   0.002   PHE A 486 
 TYR   0.025   0.002   TYR D 158 
 ARG   0.004   0.001   ARG D 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01055 (    7)
  link_NAG-ASN         : angle       7.71272 (   21)
  hydrogen bonds       : bond        0.04638 (  322)
  hydrogen bonds       : angle       4.76681 (  909)
  SS BOND              : bond        0.00521 (    7)
  SS BOND              : angle       1.12025 (   14)
  covalent geometry    : bond        0.00403 ( 6727)
  covalent geometry    : angle       0.66885 ( 9143)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4174.34 seconds
wall clock time: 78 minutes 54.57 seconds (4734.57 seconds total)