Starting phenix.real_space_refine
on Sun May 11 07:22:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y0y_38823/05_2025/8y0y_38823.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y0y_38823/05_2025/8y0y_38823.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y0y_38823/05_2025/8y0y_38823.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y0y_38823/05_2025/8y0y_38823.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y0y_38823/05_2025/8y0y_38823.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y0y_38823/05_2025/8y0y_38823.cif"
  }
  resolution = 2.86
  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=   0.054
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3253 atoms to isotropic.
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      24      5.16       5
     C    3177      2.51       5
     N     849      2.21       5
     O     977      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5027
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1729
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "D"
      Number of atoms: 1741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1741
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    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
  Time building chain proxies: 3.76, per 1000 atoms: 0.75
  Number of scatterers: 5027
  At special positions: 0
  Unit cell: (84.7, 99, 90.2, 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      24     16.00
     O     977      8.00
     N     849      7.00
     C    3177      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 184 " - pdb=" SG  CYS E 249 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 318 " - pdb=" SG  CYS E 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  47 " - pdb=" SG  CYS D 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 455 " - pdb=" SG  CYS D 520 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 343 "
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 622.2 milliseconds
  

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1174

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 13 sheets defined
      9.2% alpha, 33.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'E' and resid 240 through 244
      removed outlier: 4.205A  pdb=" N   PHE E 244 " --> pdb=" O   ALA E 241 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 324 through 328
      removed outlier: 3.600A  pdb=" N   TYR E 328 " --> pdb=" O   PHE E 325 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 383 through 387
      removed outlier: 4.162A  pdb=" N   THR E 387 " --> pdb=" O   ALA E 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 57
      removed outlier: 4.010A  pdb=" N   ASN D  56 " --> pdb=" O   THR D  53 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   TYR D  57 " --> pdb=" O   PHE D  54 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 53 through 57'
    Processing helix  chain 'D' and resid 112 through 116
      removed outlier: 3.697A  pdb=" N   THR D 116 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 511 through 515
      removed outlier: 3.879A  pdb=" N   SER D 515 " --> pdb=" O   PRO D 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 4.254A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.712A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'E' and resid 167 through 168
      removed outlier: 3.715A  pdb=" N   VAL E 180 " --> pdb=" O   ILE E 236 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASP E 231 " --> pdb=" O   SER E 228 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 171 through 174
      removed outlier: 6.639A  pdb=" N   TRP E 196 " --> pdb=" O   LEU E 208 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 299 through 303
      removed outlier: 3.553A  pdb=" N   GLN E 299 " --> pdb=" O   SER E 321 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER E 321 " --> pdb=" O   GLN E 299 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER E 303 " --> pdb=" O   SER E 317 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 307 through 308
    Processing sheet with id=AA5, first strand: chain 'E' and resid 354 through 356
      removed outlier: 5.018A  pdb=" N   TRP E 343 " --> pdb=" O   ARG E 334 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ARG E 334 " --> pdb=" O   TRP E 343 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER E 331 " --> pdb=" O   ALA E 393 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 354 through 356
      removed outlier: 5.018A  pdb=" N   TRP E 343 " --> pdb=" O   ARG E 334 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ARG E 334 " --> pdb=" O   TRP E 343 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER E 331 " --> pdb=" O   ALA E 393 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
    Processing sheet with id=AA8, first strand: chain 'D' and resid 36 through 37
      removed outlier: 7.260A  pdb=" N   MET D  59 " --> pdb=" O   VAL D  75 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   VAL D  75 " --> pdb=" O   MET D  59 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   TRP D  61 " --> pdb=" O   VAL D  73 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 438 through 439
      removed outlier: 3.701A  pdb=" N   PHE D 503 " --> pdb=" O   CYS D 455 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ASP D 502 " --> pdb=" O   SER D 499 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 442 through 445
      removed outlier: 3.699A  pdb=" N   GLU D 537 " --> pdb=" O   LEU D 443 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA D 445 " --> pdb=" O   GLU D 537 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   LEU D 465 " --> pdb=" O   TYR D 481 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   TYR D 481 " --> pdb=" O   LEU D 465 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   TRP D 467 " --> pdb=" O   LEU D 479 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.687A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.585A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    414 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1621
        1.35 -     1.47: 1367
        1.47 -     1.59: 2129
        1.59 -     1.71: 0
        1.71 -     1.83: 32
  Bond restraints: 5149
  Sorted by residual:
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C5  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.23e+00
  bond pdb=" C3  NAG A 601 "
       pdb=" O3  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.75e-01
  bond pdb=" CG  PRO E 169 "
       pdb=" CD  PRO E 169 "
    ideal  model  delta    sigma   weight residual
    1.512  1.489  0.023 2.70e-02 1.37e+03 7.37e-01
  bond pdb=" C   LEU D 526 "
       pdb=" N   PRO D 527 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.59e-01
  ... (remaining 5144 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 6807
        1.16 -     2.32: 146
        2.32 -     3.47: 31
        3.47 -     4.63: 4
        4.63 -     5.79: 2
  Bond angle restraints: 6990
  Sorted by residual:
  angle pdb=" N   GLY E 412 "
        pdb=" CA  GLY E 412 "
        pdb=" C   GLY E 412 "
      ideal   model   delta    sigma   weight residual
     112.48  115.58   -3.10 1.21e+00 6.83e-01 6.58e+00
  angle pdb=" C   ASN D 525 "
        pdb=" N   LEU D 526 "
        pdb=" CA  LEU D 526 "
      ideal   model   delta    sigma   weight residual
     120.26  123.23   -2.97 1.34e+00 5.57e-01 4.90e+00
  angle pdb=" CA  LEU A 455 "
        pdb=" CB  LEU A 455 "
        pdb=" CG  LEU A 455 "
      ideal   model   delta    sigma   weight residual
     116.30  122.09   -5.79 3.50e+00 8.16e-02 2.74e+00
  angle pdb=" CA  GLY E 412 "
        pdb=" C   GLY E 412 "
        pdb=" O   GLY E 412 "
      ideal   model   delta    sigma   weight residual
     122.24  120.82    1.42 8.70e-01 1.32e+00 2.66e+00
  angle pdb=" CA  PRO D  39 "
        pdb=" CB  PRO D  39 "
        pdb=" CG  PRO D  39 "
      ideal   model   delta    sigma   weight residual
     104.50  107.29   -2.79 1.90e+00 2.77e-01 2.16e+00
  ... (remaining 6985 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.05: 2767
       16.05 -    32.11: 200
       32.11 -    48.16: 47
       48.16 -    64.22: 12
       64.22 -    80.27: 6
  Dihedral angle restraints: 3032
    sinusoidal: 1170
      harmonic: 1862
  Sorted by residual:
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.49   45.51     1      1.00e+01 1.00e-02 2.87e+01
  dihedral pdb=" CA  ASP D 524 "
           pdb=" CB  ASP D 524 "
           pdb=" CG  ASP D 524 "
           pdb=" OD1 ASP D 524 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.49   54.49     1      2.00e+01 2.50e-03 1.01e+01
  dihedral pdb=" CB  LYS E 206 "
           pdb=" CG  LYS E 206 "
           pdb=" CD  LYS E 206 "
           pdb=" CE  LYS E 206 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.48  -56.48     3      1.50e+01 4.44e-03 9.40e+00
  ... (remaining 3029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 417
       0.025 -    0.049: 205
       0.049 -    0.074: 59
       0.074 -    0.098: 31
       0.098 -    0.123: 40
  Chirality restraints: 752
  Sorted by residual:
  chirality pdb=" CA  ILE A 434 "
            pdb=" N   ILE A 434 "
            pdb=" C   ILE A 434 "
            pdb=" CB  ILE A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  chirality pdb=" CB  ILE E 163 "
            pdb=" CA  ILE E 163 "
            pdb=" CG1 ILE E 163 "
            pdb=" CG2 ILE E 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.12 2.00e-01 2.50e+01 3.76e-01
  chirality pdb=" CA  ILE D 480 "
            pdb=" N   ILE D 480 "
            pdb=" C   ILE D 480 "
            pdb=" CB  ILE D 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.69e-01
  ... (remaining 749 not shown)

  Planarity restraints: 906
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN E 309 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO E 310 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO E 310 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO E 310 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 134 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO D 135 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO D 135 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D 135 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D  38 "   -0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO D  39 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO D  39 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D  39 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 903 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1467
        2.81 -     3.34: 3744
        3.34 -     3.86: 7623
        3.86 -     4.38: 8663
        4.38 -     4.90: 16227
  Nonbonded interactions: 37724
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER E 345 "
            pdb=" O   TYR E 355 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" OE1 GLU A 406 "
            pdb=" OH  TYR A 495 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OE2 GLU E 404 "
            pdb=" ND2 ASN A 450 "
     model   vdw
     2.368 3.120
  nonbonded pdb=" O   PHE D  54 "
            pdb=" NH2 ARG D  97 "
     model   vdw
     2.428 3.120
  ... (remaining 37719 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.330
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
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      :  0.002   0.027   5158  Z= 0.098
  Angle     :  0.450   5.789   7009  Z= 0.246
  Chirality :  0.041   0.123    752
  Planarity :  0.004   0.037    905
  Dihedral  : 12.370  80.272   1834
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.37 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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:  0.04 (0.33), residues: 642
  helix: -2.71 (0.98), residues: 19
  sheet:  1.30 (0.35), residues: 235
  loop : -0.66 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E 343 
 HIS   0.001   0.000   HIS D  60 
 PHE   0.005   0.001   PHE A 490 
 TYR   0.006   0.001   TYR E 210 
 ARG   0.003   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00299 (    1)
  link_NAG-ASN         : angle       0.55955 (    3)
  hydrogen bonds       : bond        0.29114 (  157)
  hydrogen bonds       : angle       9.27533 (  414)
  SS BOND              : bond        0.00313 (    8)
  SS BOND              : angle       0.75450 (   16)
  covalent geometry    : bond        0.00179 ( 5149)
  covalent geometry    : angle       0.44885 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.487 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 81
  average time/residue: 1.0488
  time to fit residues: 89.1007
Evaluate side-chains
  60 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.3980
   chunk 36 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
E 214 ASN
E 373 ASN
E 411 GLN
D 102 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.163624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.138560 restraints weight = 5957.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 2.02
r_work: 0.3603 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3501 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5158  Z= 0.131
  Angle     :  0.645  12.446   7009  Z= 0.340
  Chirality :  0.047   0.232    752
  Planarity :  0.004   0.037    905
  Dihedral  :  4.254  24.900    736
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.43 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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: -0.29 (0.33), residues: 642
  helix: -2.88 (0.80), residues: 27
  sheet:  1.13 (0.35), residues: 244
  loop : -0.94 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS D  60 
 PHE   0.014   0.001   PHE A 377 
 TYR   0.015   0.002   TYR E 210 
 ARG   0.004   0.001   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00258 (    1)
  link_NAG-ASN         : angle       0.89695 (    3)
  hydrogen bonds       : bond        0.04123 (  157)
  hydrogen bonds       : angle       5.91411 (  414)
  SS BOND              : bond        0.00816 (    8)
  SS BOND              : angle       3.34122 (   16)
  covalent geometry    : bond        0.00294 ( 5149)
  covalent geometry    : angle       0.62519 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.519 
Fit side-chains
REVERT: E  379 MET cc_start: 0.7318 (ptt) cc_final: 0.7017 (ptt)
REVERT: D   90 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8025 (tptt)
  outliers start: 11
  outliers final: 7
  residues processed: 72
  average time/residue: 1.1069
  time to fit residues: 83.3996
Evaluate side-chains
  64 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain E residue  170 SER
Chi-restraints excluded: chain E residue  411 GLN
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  441 SER
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  380 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   chunk 56 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0070
   chunk 31 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.8802

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

Flipped N/Q/H residues before XYZ refinement:
E 214 ASN
E 373 ASN
E 407 HIS
E 411 GLN
D 102 ASN
A 501 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.158720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.133270 restraints weight = 5979.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.02
r_work: 0.3541 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5158  Z= 0.150
  Angle     :  0.656  10.263   7009  Z= 0.350
  Chirality :  0.047   0.186    752
  Planarity :  0.005   0.041    905
  Dihedral  :  4.495  20.065    736
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  :  9.24 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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: -0.46 (0.33), residues: 642
  helix: -3.12 (0.91), residues: 21
  sheet:  1.16 (0.34), residues: 249
  loop : -1.24 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.004   0.001   HIS E 407 
 PHE   0.010   0.001   PHE A 377 
 TYR   0.015   0.002   TYR E 210 
 ARG   0.003   0.001   ARG D 493 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00142 (    1)
  link_NAG-ASN         : angle       1.19996 (    3)
  hydrogen bonds       : bond        0.04526 (  157)
  hydrogen bonds       : angle       5.68916 (  414)
  SS BOND              : bond        0.00581 (    8)
  SS BOND              : angle       3.33878 (   16)
  covalent geometry    : bond        0.00338 ( 5149)
  covalent geometry    : angle       0.63696 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 1.180 
Fit side-chains
REVERT: E  299 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7575 (mm110)
REVERT: E  342 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7795 (tt0)
REVERT: D   59 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7683 (mmm)
REVERT: D   90 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8123 (tptt)
REVERT: D  449 ASP cc_start: 0.6416 (m-30) cc_final: 0.6121 (m-30)
REVERT: D  493 ARG cc_start: 0.7330 (mtm110) cc_final: 0.6954 (mtm-85)
REVERT: A  462 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7781 (mptp)
  outliers start: 23
  outliers final: 8
  residues processed: 76
  average time/residue: 1.1654
  time to fit residues: 92.5295
Evaluate side-chains
  71 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain E residue  170 SER
Chi-restraints excluded: chain E residue  299 GLN
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue   90 LYS
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  441 SER
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  462 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    0.1980
   chunk 54 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
E 188 GLN
E 214 ASN
E 373 ASN
E 411 GLN
D 102 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.158803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.133764 restraints weight = 6072.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.98
r_work: 0.3542 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5158  Z= 0.125
  Angle     :  0.598   9.081   7009  Z= 0.320
  Chirality :  0.046   0.160    752
  Planarity :  0.004   0.041    905
  Dihedral  :  4.270  17.204    736
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  :  9.43 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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: -0.63 (0.33), residues: 642
  helix: -2.92 (0.80), residues: 27
  sheet:  0.98 (0.34), residues: 252
  loop : -1.31 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D  60 
 PHE   0.008   0.001   PHE A 377 
 TYR   0.014   0.002   TYR E 391 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00160 (    1)
  link_NAG-ASN         : angle       1.30172 (    3)
  hydrogen bonds       : bond        0.03956 (  157)
  hydrogen bonds       : angle       5.46297 (  414)
  SS BOND              : bond        0.00576 (    8)
  SS BOND              : angle       3.08135 (   16)
  covalent geometry    : bond        0.00277 ( 5149)
  covalent geometry    : angle       0.57998 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.567 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8140 (pp30)
REVERT: E  253 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7310 (t0)
REVERT: E  299 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7514 (mm110)
REVERT: E  342 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7759 (tt0)
REVERT: E  398 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8121 (mt)
REVERT: D   59 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7650 (mmm)
REVERT: D   68 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7485 (mptt)
REVERT: D  449 ASP cc_start: 0.6319 (m-30) cc_final: 0.6031 (m-30)
REVERT: D  493 ARG cc_start: 0.7358 (mtm110) cc_final: 0.6975 (mtm-85)
REVERT: D  535 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7842 (tptm)
REVERT: A  382 VAL cc_start: 0.6321 (OUTLIER) cc_final: 0.6027 (p)
REVERT: A  455 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7717 (tt)
REVERT: A  462 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7761 (mptp)
  outliers start: 29
  outliers final: 10
  residues processed: 78
  average time/residue: 1.0951
  time to fit residues: 89.4121
Evaluate side-chains
  74 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 53
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain E residue  250 GLN
Chi-restraints excluded: chain E residue  253 ASP
Chi-restraints excluded: chain E residue  299 GLN
Chi-restraints excluded: chain E residue  307 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  392 CYS
Chi-restraints excluded: chain E residue  398 ILE
Chi-restraints excluded: chain E residue  411 GLN
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  441 SER
Chi-restraints excluded: chain D residue  535 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  462 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
E 188 GLN
E 214 ASN
E 373 ASN
D 102 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.158210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.132636 restraints weight = 5930.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.02
r_work: 0.3517 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5158  Z= 0.141
  Angle     :  0.623   9.084   7009  Z= 0.333
  Chirality :  0.046   0.167    752
  Planarity :  0.005   0.044    905
  Dihedral  :  4.400  17.408    736
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  5.55 %
    Allowed  : 10.91 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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: -0.69 (0.32), residues: 642
  helix: -2.71 (0.89), residues: 21
  sheet:  0.89 (0.33), residues: 252
  loop : -1.37 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS D  60 
 PHE   0.009   0.001   PHE A 377 
 TYR   0.014   0.002   TYR E 210 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00170 (    1)
  link_NAG-ASN         : angle       1.26828 (    3)
  hydrogen bonds       : bond        0.04141 (  157)
  hydrogen bonds       : angle       5.47666 (  414)
  SS BOND              : bond        0.00658 (    8)
  SS BOND              : angle       3.17488 (   16)
  covalent geometry    : bond        0.00318 ( 5149)
  covalent geometry    : angle       0.60436 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 56
  time to evaluate  : 0.494 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8062 (pp30)
REVERT: E  253 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7197 (t0)
REVERT: E  299 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7404 (mm110)
REVERT: E  342 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7830 (tt0)
REVERT: E  398 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8143 (mt)
REVERT: E  411 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6110 (pt0)
REVERT: D   59 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7722 (mmm)
REVERT: D   68 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7520 (mptt)
REVERT: D  449 ASP cc_start: 0.6356 (m-30) cc_final: 0.6102 (m-30)
REVERT: D  493 ARG cc_start: 0.7394 (mtm110) cc_final: 0.6946 (mtm-85)
REVERT: D  535 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7842 (tptm)
REVERT: A  382 VAL cc_start: 0.6219 (OUTLIER) cc_final: 0.5949 (p)
REVERT: A  455 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7716 (tt)
REVERT: A  462 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7805 (mptp)
  outliers start: 30
  outliers final: 14
  residues processed: 77
  average time/residue: 1.0531
  time to fit residues: 85.0385
Evaluate side-chains
  81 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 55
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain E residue  250 GLN
Chi-restraints excluded: chain E residue  253 ASP
Chi-restraints excluded: chain E residue  299 GLN
Chi-restraints excluded: chain E residue  307 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  379 MET
Chi-restraints excluded: chain E residue  392 CYS
Chi-restraints excluded: chain E residue  398 ILE
Chi-restraints excluded: chain E residue  411 GLN
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  108 MET
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  441 SER
Chi-restraints excluded: chain D residue  488 THR
Chi-restraints excluded: chain D residue  521 GLN
Chi-restraints excluded: chain D residue  535 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  462 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 26 optimal weight:    0.0870
   chunk 54 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 3 optimal weight:    0.7980
   overall best weight:    1.0362

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

Flipped N/Q/H residues before XYZ refinement:
E 188 GLN
E 214 ASN
E 380 ASN
E 411 GLN
D 102 ASN
D 104 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.155978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.130536 restraints weight = 5987.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.02
r_work: 0.3498 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5158  Z= 0.165
  Angle     :  0.667   9.787   7009  Z= 0.358
  Chirality :  0.048   0.172    752
  Planarity :  0.005   0.047    905
  Dihedral  :  4.642  18.887    736
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  5.55 %
    Allowed  : 11.46 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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: -0.84 (0.32), residues: 642
  helix: -2.54 (0.95), residues: 21
  sheet:  0.77 (0.33), residues: 264
  loop : -1.56 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 436 
 HIS   0.005   0.001   HIS D  60 
 PHE   0.011   0.002   PHE A 377 
 TYR   0.015   0.002   TYR E 210 
 ARG   0.003   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00118 (    1)
  link_NAG-ASN         : angle       1.41583 (    3)
  hydrogen bonds       : bond        0.04443 (  157)
  hydrogen bonds       : angle       5.63824 (  414)
  SS BOND              : bond        0.00744 (    8)
  SS BOND              : angle       3.33884 (   16)
  covalent geometry    : bond        0.00380 ( 5149)
  covalent geometry    : angle       0.64783 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 61
  time to evaluate  : 0.558 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8107 (pp30)
REVERT: E  299 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7518 (mm110)
REVERT: E  342 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7814 (tt0)
REVERT: E  398 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8155 (mt)
REVERT: D   31 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6381 (mm-30)
REVERT: D   59 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7646 (mmm)
REVERT: D  449 ASP cc_start: 0.6523 (m-30) cc_final: 0.6231 (m-30)
REVERT: D  535 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7961 (tptm)
REVERT: A  382 VAL cc_start: 0.6190 (OUTLIER) cc_final: 0.5903 (p)
REVERT: A  455 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7727 (tt)
REVERT: A  462 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7913 (mptp)
  outliers start: 30
  outliers final: 17
  residues processed: 81
  average time/residue: 1.1241
  time to fit residues: 95.3364
Evaluate side-chains
  82 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 55
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain E residue  250 GLN
Chi-restraints excluded: chain E residue  253 ASP
Chi-restraints excluded: chain E residue  299 GLN
Chi-restraints excluded: chain E residue  307 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  379 MET
Chi-restraints excluded: chain E residue  392 CYS
Chi-restraints excluded: chain E residue  398 ILE
Chi-restraints excluded: chain E residue  411 GLN
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   31 GLU
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  108 MET
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  439 SER
Chi-restraints excluded: chain D residue  441 SER
Chi-restraints excluded: chain D residue  488 THR
Chi-restraints excluded: chain D residue  521 GLN
Chi-restraints excluded: chain D residue  535 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  462 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 28 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
E 214 ASN
D 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.156570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.131185 restraints weight = 5948.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.01
r_work: 0.3509 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5158  Z= 0.139
  Angle     :  0.645  10.750   7009  Z= 0.339
  Chirality :  0.047   0.169    752
  Planarity :  0.005   0.050    905
  Dihedral  :  4.492  18.488    736
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 12.57 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    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: -0.89 (0.33), residues: 642
  helix: -2.39 (0.99), residues: 21
  sheet:  0.57 (0.32), residues: 275
  loop : -1.51 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS D  60 
 PHE   0.008   0.001   PHE A 400 
 TYR   0.014   0.002   TYR E 391 
 ARG   0.003   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00171 (    1)
  link_NAG-ASN         : angle       1.41019 (    3)
  hydrogen bonds       : bond        0.04070 (  157)
  hydrogen bonds       : angle       5.52930 (  414)
  SS BOND              : bond        0.00643 (    8)
  SS BOND              : angle       3.15124 (   16)
  covalent geometry    : bond        0.00313 ( 5149)
  covalent geometry    : angle       0.62752 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 57
  time to evaluate  : 0.526 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8053 (pp30)
REVERT: E  253 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7219 (t0)
REVERT: E  299 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7418 (mm110)
REVERT: E  342 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7791 (tt0)
REVERT: E  398 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8136 (mt)
REVERT: E  411 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6346 (pt0)
REVERT: D   59 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7690 (mmm)
REVERT: D  449 ASP cc_start: 0.6385 (m-30) cc_final: 0.6116 (m-30)
REVERT: D  535 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7853 (tptm)
REVERT: A  455 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7671 (tt)
REVERT: A  462 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7892 (mptp)
  outliers start: 32
  outliers final: 16
  residues processed: 80
  average time/residue: 1.0021
  time to fit residues: 84.2582
Evaluate side-chains
  81 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 55
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain E residue  250 GLN
Chi-restraints excluded: chain E residue  253 ASP
Chi-restraints excluded: chain E residue  299 GLN
Chi-restraints excluded: chain E residue  307 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  392 CYS
Chi-restraints excluded: chain E residue  398 ILE
Chi-restraints excluded: chain E residue  411 GLN
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  108 MET
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  439 SER
Chi-restraints excluded: chain D residue  441 SER
Chi-restraints excluded: chain D residue  465 LEU
Chi-restraints excluded: chain D residue  488 THR
Chi-restraints excluded: chain D residue  521 GLN
Chi-restraints excluded: chain D residue  535 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  462 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0670
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.1524

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

Flipped N/Q/H residues before XYZ refinement:
E 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.154414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.129334 restraints weight = 6017.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.00
r_work: 0.3485 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5158  Z= 0.179
  Angle     :  0.702   9.818   7009  Z= 0.372
  Chirality :  0.048   0.180    752
  Planarity :  0.005   0.054    905
  Dihedral  :  4.751  19.104    736
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  5.55 %
    Allowed  : 12.75 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.33), residues: 642
  helix: -2.49 (1.01), residues: 21
  sheet:  0.51 (0.33), residues: 270
  loop : -1.55 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 436 
 HIS   0.005   0.001   HIS D  60 
 PHE   0.010   0.002   PHE A 377 
 TYR   0.015   0.002   TYR E 391 
 ARG   0.003   0.000   ARG D  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00127 (    1)
  link_NAG-ASN         : angle       1.47194 (    3)
  hydrogen bonds       : bond        0.04574 (  157)
  hydrogen bonds       : angle       5.67375 (  414)
  SS BOND              : bond        0.00783 (    8)
  SS BOND              : angle       3.36878 (   16)
  covalent geometry    : bond        0.00416 ( 5149)
  covalent geometry    : angle       0.68311 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 57
  time to evaluate  : 0.546 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8136 (pp30)
REVERT: E  299 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7476 (mm110)
REVERT: E  342 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7808 (tt0)
REVERT: E  398 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8156 (mt)
REVERT: E  411 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6128 (pt0)
REVERT: D   59 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7672 (mmm)
REVERT: D  449 ASP cc_start: 0.6591 (m-30) cc_final: 0.6266 (m-30)
REVERT: D  535 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7985 (tptm)
REVERT: A  455 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7774 (tt)
REVERT: A  462 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7878 (mptp)
  outliers start: 30
  outliers final: 19
  residues processed: 79
  average time/residue: 0.9904
  time to fit residues: 82.3907
Evaluate side-chains
  81 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 53
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain E residue  250 GLN
Chi-restraints excluded: chain E residue  253 ASP
Chi-restraints excluded: chain E residue  299 GLN
Chi-restraints excluded: chain E residue  307 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  392 CYS
Chi-restraints excluded: chain E residue  398 ILE
Chi-restraints excluded: chain E residue  411 GLN
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  108 MET
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  439 SER
Chi-restraints excluded: chain D residue  441 SER
Chi-restraints excluded: chain D residue  465 LEU
Chi-restraints excluded: chain D residue  488 THR
Chi-restraints excluded: chain D residue  521 GLN
Chi-restraints excluded: chain D residue  535 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  462 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E 214 ASN
D  28 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.156989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.131780 restraints weight = 5950.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 2.00
r_work: 0.3509 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5158  Z= 0.132
  Angle     :  0.632   8.973   7009  Z= 0.334
  Chirality :  0.046   0.164    752
  Planarity :  0.005   0.053    905
  Dihedral  :  4.456  18.331    736
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 13.68 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.33), residues: 642
  helix: -2.42 (1.00), residues: 21
  sheet:  0.52 (0.33), residues: 270
  loop : -1.53 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS D  60 
 PHE   0.008   0.001   PHE A 400 
 TYR   0.014   0.002   TYR E 391 
 ARG   0.004   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00173 (    1)
  link_NAG-ASN         : angle       1.48642 (    3)
  hydrogen bonds       : bond        0.03945 (  157)
  hydrogen bonds       : angle       5.47887 (  414)
  SS BOND              : bond        0.00611 (    8)
  SS BOND              : angle       3.05794 (   16)
  covalent geometry    : bond        0.00297 ( 5149)
  covalent geometry    : angle       0.61506 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 52
  time to evaluate  : 0.566 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8111 (pp30)
REVERT: E  253 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7300 (t0)
REVERT: E  299 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7390 (mm110)
REVERT: E  342 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7820 (tt0)
REVERT: E  398 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8153 (mt)
REVERT: E  411 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6101 (pt0)
REVERT: D   59 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7724 (mmm)
REVERT: D  449 ASP cc_start: 0.6383 (m-30) cc_final: 0.6109 (m-30)
REVERT: D  535 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7862 (tptm)
REVERT: A  455 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7708 (tt)
REVERT: A  462 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7819 (mptp)
  outliers start: 28
  outliers final: 16
  residues processed: 73
  average time/residue: 0.9957
  time to fit residues: 76.5067
Evaluate side-chains
  75 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 49
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain E residue  250 GLN
Chi-restraints excluded: chain E residue  253 ASP
Chi-restraints excluded: chain E residue  299 GLN
Chi-restraints excluded: chain E residue  307 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  392 CYS
Chi-restraints excluded: chain E residue  398 ILE
Chi-restraints excluded: chain E residue  411 GLN
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue  108 MET
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  439 SER
Chi-restraints excluded: chain D residue  441 SER
Chi-restraints excluded: chain D residue  488 THR
Chi-restraints excluded: chain D residue  521 GLN
Chi-restraints excluded: chain D residue  535 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  462 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0870
   chunk 52 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0060
   overall best weight:    0.6174

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

Flipped N/Q/H residues before XYZ refinement:
E 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.157403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.132445 restraints weight = 5930.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.00
r_work: 0.3517 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5158  Z= 0.119
  Angle     :  0.608   8.528   7009  Z= 0.320
  Chirality :  0.046   0.157    752
  Planarity :  0.005   0.051    905
  Dihedral  :  4.312  17.636    736
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 14.23 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.33), residues: 642
  helix: -2.34 (1.01), residues: 21
  sheet:  0.60 (0.32), residues: 272
  loop : -1.56 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D  60 
 PHE   0.008   0.001   PHE A 400 
 TYR   0.014   0.001   TYR E 391 
 ARG   0.003   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    1)
  link_NAG-ASN         : angle       1.39397 (    3)
  hydrogen bonds       : bond        0.03725 (  157)
  hydrogen bonds       : angle       5.35068 (  414)
  SS BOND              : bond        0.00548 (    8)
  SS BOND              : angle       2.92029 (   16)
  covalent geometry    : bond        0.00265 ( 5149)
  covalent geometry    : angle       0.59209 ( 6990)

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

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

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1284 Ramachandran restraints generated.
    642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 52
  time to evaluate  : 0.579 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8137 (pp30)
REVERT: E  253 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7408 (t0)
REVERT: E  299 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7397 (mm110)
REVERT: E  342 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7819 (tt0)
REVERT: E  411 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5984 (pt0)
REVERT: D   59 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7694 (mmm)
REVERT: D  449 ASP cc_start: 0.6260 (m-30) cc_final: 0.6005 (m-30)
REVERT: D  535 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7870 (tptm)
REVERT: A  455 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7698 (tt)
REVERT: A  462 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7922 (mptp)
  outliers start: 27
  outliers final: 17
  residues processed: 72
  average time/residue: 1.0083
  time to fit residues: 76.4168
Evaluate side-chains
  75 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 49
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain E residue  250 GLN
Chi-restraints excluded: chain E residue  253 ASP
Chi-restraints excluded: chain E residue  299 GLN
Chi-restraints excluded: chain E residue  307 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  392 CYS
Chi-restraints excluded: chain E residue  411 GLN
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  108 MET
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  439 SER
Chi-restraints excluded: chain D residue  441 SER
Chi-restraints excluded: chain D residue  488 THR
Chi-restraints excluded: chain D residue  521 GLN
Chi-restraints excluded: chain D residue  535 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  462 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 26 optimal weight:    0.3980
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E 411 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.156804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.131645 restraints weight = 6105.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.00
r_work: 0.3508 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5158  Z= 0.132
  Angle     :  0.627   8.680   7009  Z= 0.331
  Chirality :  0.046   0.161    752
  Planarity :  0.005   0.053    905
  Dihedral  :  4.396  17.885    736
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 14.05 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.33), residues: 642
  helix: -2.38 (1.00), residues: 21
  sheet:  0.56 (0.33), residues: 269
  loop : -1.50 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D  60 
 PHE   0.009   0.001   PHE A 400 
 TYR   0.015   0.002   TYR E 210 
 ARG   0.003   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00232 (    1)
  link_NAG-ASN         : angle       1.39186 (    3)
  hydrogen bonds       : bond        0.03878 (  157)
  hydrogen bonds       : angle       5.39359 (  414)
  SS BOND              : bond        0.00618 (    8)
  SS BOND              : angle       3.02735 (   16)
  covalent geometry    : bond        0.00299 ( 5149)
  covalent geometry    : angle       0.61024 ( 6990)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3846.82 seconds
wall clock time: 66 minutes 56.69 seconds (4016.69 seconds total)