Starting phenix.real_space_refine
on Mon Apr 28 14:49:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y0y_38823/04_2025/8y0y_38823.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y0y_38823/04_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_38823/04_2025/8y0y_38823.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y0y_38823/04_2025/8y0y_38823.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y0y_38823/04_2025/8y0y_38823.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y0y_38823/04_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 3.82, per 1000 atoms: 0.76
  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: 1.17
  Conformation dependent library (CDL) restraints added in 640.4 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: 0.73
  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: 1.64

  Time building geometry restraints manager: 1.41 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:             1.760
  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:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.860
  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:             0.000
  Load rotamer database and sin/cos tables:13.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.020
-------------------------------------------------------------------------------
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  : 0.583 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 81
  average time/residue: 1.0703
  time to fit residues: 90.8769
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  : 0.571 
-------------------------------------------------------------------------------
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 = 28)----------------|
| 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  : 0.537 
Fit side-chains
REVERT: E  379 MET cc_start: 0.7319 (ptt) cc_final: 0.7018 (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: 1.1041
  time to fit residues: 83.1896
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  : 0.518 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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
D 102 ASN
A 501 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.158718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.133219 restraints weight = 5984.461|
|-----------------------------------------------------------------------------|
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: 0.3437 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5158  Z= 0.152
  Angle     :  0.656  10.328   7009  Z= 0.349
  Chirality :  0.047   0.188    752
  Planarity :  0.005   0.041    905
  Dihedral  :  4.493  20.229    736
  Min Nonbonded Distance : 2.425

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: -3.11 (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 D  60 
 PHE   0.008   0.001   PHE D 530 
 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        0.00166 (    1)
  link_NAG-ASN         : angle       1.18226 (    3)
  hydrogen bonds       : bond        0.04527 (  157)
  hydrogen bonds       : angle       5.69376 (  414)
  SS BOND              : bond        0.00599 (    8)
  SS BOND              : angle       3.32078 (   16)
  covalent geometry    : bond        0.00341 ( 5149)
  covalent geometry    : angle       0.63714 ( 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
  87 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.508 
Fit side-chains
REVERT: E  299 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7575 (mm110)
REVERT: E  342 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7812 (tt0)
REVERT: D   59 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7694 (mmm)
REVERT: D   68 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7168 (mptt)
REVERT: D   90 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8129 (tptt)
REVERT: D  449 ASP cc_start: 0.6615 (m-30) cc_final: 0.6280 (m-30)
REVERT: D  493 ARG cc_start: 0.7337 (mtm110) cc_final: 0.6954 (mtm-85)
REVERT: A  462 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7756 (mptp)
  outliers start: 23
  outliers final: 9
  residues processed: 76
  average time/residue: 1.1374
  time to fit residues: 90.7085
Evaluate side-chains
  73 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
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  307 LEU
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain D residue   59 MET
Chi-restraints excluded: chain D residue   68 LYS
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:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0370
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.8862

-------------------------------------------------------------------------------
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 380 ASN
E 411 GLN
D 102 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.157166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.131680 restraints weight = 5984.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.04
r_work: 0.3512 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3406 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2807

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= 0.149
  Angle     :  0.644   9.621   7009  Z= 0.344
  Chirality :  0.047   0.169    752
  Planarity :  0.005   0.044    905
  Dihedral  :  4.509  18.257    736
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  :  9.80 %
    Favored  : 84.84 %
  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: -0.72 (0.32), residues: 642
  helix: -2.99 (0.79), residues: 27
  sheet:  0.93 (0.33), residues: 264
  loop : -1.47 (0.30), 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   0.010   0.001   PHE A 377 
 TYR   0.015   0.002   TYR E 391 
 ARG   0.004   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00142 (    1)
  link_NAG-ASN         : angle       1.32703 (    3)
  hydrogen bonds       : bond        0.04274 (  157)
  hydrogen bonds       : angle       5.60130 (  414)
  SS BOND              : bond        0.00651 (    8)
  SS BOND              : angle       3.24714 (   16)
  covalent geometry    : bond        0.00338 ( 5149)
  covalent geometry    : angle       0.62575 ( 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
  88 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 59
  time to evaluate  : 0.594 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7989 (pt0)
REVERT: E  253 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7916 (p0)
REVERT: E  299 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7389 (mm110)
REVERT: E  342 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7812 (tt0)
REVERT: E  398 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8113 (mt)
REVERT: D   59 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7743 (mmm)
REVERT: D  449 ASP cc_start: 0.6490 (m-30) cc_final: 0.6232 (m-30)
REVERT: D  493 ARG cc_start: 0.7378 (mtm110) cc_final: 0.6940 (mtm-85)
REVERT: D  535 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7877 (tptm)
REVERT: A  382 VAL cc_start: 0.6228 (OUTLIER) cc_final: 0.5948 (p)
REVERT: A  455 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7686 (tt)
REVERT: A  462 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7771 (mptp)
  outliers start: 29
  outliers final: 9
  residues processed: 79
  average time/residue: 1.1985
  time to fit residues: 99.0829
Evaluate side-chains
  75 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
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  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  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:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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
D 102 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.157530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.132011 restraints weight = 5989.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.02
r_work: 0.3519 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2864

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= 0.136
  Angle     :  0.621   9.250   7009  Z= 0.332
  Chirality :  0.046   0.168    752
  Planarity :  0.005   0.046    905
  Dihedral  :  4.430  17.980    736
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 10.91 %
    Favored  : 83.36 %
  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: -0.81 (0.32), residues: 642
  helix: -2.67 (0.92), residues: 21
  sheet:  0.66 (0.33), residues: 263
  loop : -1.39 (0.30), residues: 358

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 210 
 ARG   0.002   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00154 (    1)
  link_NAG-ASN         : angle       1.35466 (    3)
  hydrogen bonds       : bond        0.04082 (  157)
  hydrogen bonds       : angle       5.49367 (  414)
  SS BOND              : bond        0.00624 (    8)
  SS BOND              : angle       3.16002 (   16)
  covalent geometry    : bond        0.00306 ( 5149)
  covalent geometry    : angle       0.60226 ( 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
  89 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 58
  time to evaluate  : 0.706 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8051 (pp30)
REVERT: E  253 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7233 (t0)
REVERT: E  299 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7413 (mm110)
REVERT: E  342 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7803 (tt0)
REVERT: E  398 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8139 (mt)
REVERT: E  411 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.5743 (pp30)
REVERT: D   31 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6497 (mm-30)
REVERT: D   59 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7716 (mmm)
REVERT: D   68 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7543 (mptt)
REVERT: D  449 ASP cc_start: 0.6382 (m-30) cc_final: 0.6132 (m-30)
REVERT: D  535 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7863 (tptm)
REVERT: A  382 VAL cc_start: 0.6230 (OUTLIER) cc_final: 0.5979 (p)
REVERT: A  455 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7718 (tt)
REVERT: A  462 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7864 (mptp)
  outliers start: 31
  outliers final: 15
  residues processed: 80
  average time/residue: 1.6136
  time to fit residues: 134.7803
Evaluate side-chains
  83 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 55
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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   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  405 ASP
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:    3.9990
   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:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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
D 102 ASN
D 104 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.154022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.128631 restraints weight = 5996.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.03
r_work: 0.3476 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3373 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5158  Z= 0.198
  Angle     :  0.722  10.644   7009  Z= 0.386
  Chirality :  0.049   0.185    752
  Planarity :  0.005   0.054    905
  Dihedral  :  4.875  19.555    736
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 11.83 %
    Favored  : 82.07 %
  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: -1.01 (0.32), residues: 642
  helix: -2.62 (0.95), residues: 21
  sheet:  0.46 (0.32), residues: 278
  loop : -1.56 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 436 
 HIS   0.006   0.002   HIS D  60 
 PHE   0.011   0.002   PHE A 377 
 TYR   0.016   0.002   TYR E 391 
 ARG   0.003   0.001   ARG D  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00095 (    1)
  link_NAG-ASN         : angle       1.44581 (    3)
  hydrogen bonds       : bond        0.04846 (  157)
  hydrogen bonds       : angle       5.80083 (  414)
  SS BOND              : bond        0.00858 (    8)
  SS BOND              : angle       3.54195 (   16)
  covalent geometry    : bond        0.00464 ( 5149)
  covalent geometry    : angle       0.70196 ( 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
  92 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 59
  time to evaluate  : 1.030 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7884 (tm-30)
REVERT: E  299 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7580 (mm110)
REVERT: E  342 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7761 (tt0)
REVERT: E  398 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8160 (mt)
REVERT: E  411 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.5755 (pp30)
REVERT: D   31 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6546 (mm-30)
REVERT: D   59 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7749 (mmm)
REVERT: D  449 ASP cc_start: 0.6745 (m-30) cc_final: 0.6449 (m-30)
REVERT: D  535 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7922 (tptm)
REVERT: A  455 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7799 (tt)
  outliers start: 33
  outliers final: 18
  residues processed: 82
  average time/residue: 1.5209
  time to fit residues: 130.8742
Evaluate side-chains
  84 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 57
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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  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  382 VAL
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 28 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 11 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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
D 102 ASN
** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.157870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.132561 restraints weight = 5898.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.01
r_work: 0.3517 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5158  Z= 0.117
  Angle     :  0.613  11.077   7009  Z= 0.322
  Chirality :  0.045   0.156    752
  Planarity :  0.005   0.051    905
  Dihedral  :  4.354  18.082    736
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 12.38 %
    Favored  : 81.89 %
  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: -2.24 (1.04), residues: 21
  sheet:  0.57 (0.32), residues: 274
  loop : -1.54 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   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   0.002   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00178 (    1)
  link_NAG-ASN         : angle       1.43891 (    3)
  hydrogen bonds       : bond        0.03745 (  157)
  hydrogen bonds       : angle       5.43416 (  414)
  SS BOND              : bond        0.00530 (    8)
  SS BOND              : angle       2.98287 (   16)
  covalent geometry    : bond        0.00256 ( 5149)
  covalent geometry    : angle       0.59637 ( 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
  86 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 55
  time to evaluate  : 0.578 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8071 (pp30)
REVERT: E  253 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7453 (t0)
REVERT: E  299 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7385 (mm110)
REVERT: E  342 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7797 (tt0)
REVERT: E  411 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.5638 (pp30)
REVERT: D   59 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7638 (mmm)
REVERT: D   68 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7548 (mptt)
REVERT: D  449 ASP cc_start: 0.6330 (m-30) cc_final: 0.6058 (m-30)
REVERT: D  535 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7855 (tptm)
REVERT: A  455 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7668 (tt)
REVERT: A  462 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7869 (mptp)
  outliers start: 31
  outliers final: 16
  residues processed: 76
  average time/residue: 1.1628
  time to fit residues: 92.4990
Evaluate side-chains
  76 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 50
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0870
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 54 optimal weight:    0.6980
   chunk 10 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    0.1980
   overall best weight:    0.3236

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.160545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.135117 restraints weight = 5993.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.04
r_work: 0.3552 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5158  Z= 0.092
  Angle     :  0.551  10.321   7009  Z= 0.288
  Chirality :  0.044   0.150    752
  Planarity :  0.004   0.046    905
  Dihedral  :  3.967  16.057    736
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 14.23 %
    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: -0.78 (0.33), residues: 642
  helix: -2.14 (1.03), residues: 21
  sheet:  0.64 (0.33), residues: 261
  loop : -1.36 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.000   HIS D  60 
 PHE   0.007   0.001   PHE A 400 
 TYR   0.014   0.001   TYR A 380 
 ARG   0.002   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00225 (    1)
  link_NAG-ASN         : angle       1.29655 (    3)
  hydrogen bonds       : bond        0.03195 (  157)
  hydrogen bonds       : angle       5.15957 (  414)
  SS BOND              : bond        0.00405 (    8)
  SS BOND              : angle       2.58966 (   16)
  covalent geometry    : bond        0.00196 ( 5149)
  covalent geometry    : angle       0.53739 ( 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
  77 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.530 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7941 (pt0)
REVERT: E  398 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8125 (mt)
REVERT: D   68 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7491 (mptt)
REVERT: A  455 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7649 (tt)
  outliers start: 23
  outliers final: 10
  residues processed: 71
  average time/residue: 1.0298
  time to fit residues: 77.1730
Evaluate side-chains
  62 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
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  307 LEU
Chi-restraints excluded: chain E residue  398 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  437 THR
Chi-restraints excluded: chain D residue  439 SER
Chi-restraints excluded: chain D residue  488 THR
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  455 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
E 411 GLN
D  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.155777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130278 restraints weight = 5953.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.02
r_work: 0.3487 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5158  Z= 0.156
  Angle     :  0.663   9.214   7009  Z= 0.349
  Chirality :  0.047   0.166    752
  Planarity :  0.005   0.050    905
  Dihedral  :  4.483  18.142    736
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 14.79 %
    Favored  : 80.96 %
  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: -0.87 (0.33), residues: 642
  helix: -2.28 (1.05), residues: 21
  sheet:  0.59 (0.33), residues: 270
  loop : -1.47 (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   0.001   PHE E 255 
 TYR   0.014   0.002   TYR E 391 
 ARG   0.003   0.000   ARG D  97 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    1)
  link_NAG-ASN         : angle       1.31085 (    3)
  hydrogen bonds       : bond        0.04182 (  157)
  hydrogen bonds       : angle       5.46777 (  414)
  SS BOND              : bond        0.00716 (    8)
  SS BOND              : angle       3.16649 (   16)
  covalent geometry    : bond        0.00358 ( 5149)
  covalent geometry    : angle       0.64586 ( 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
  82 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.570 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8108 (pp30)
REVERT: E  299 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7364 (mm110)
REVERT: E  398 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8130 (mt)
REVERT: D   68 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7526 (mptt)
REVERT: A  455 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7703 (tt)
  outliers start: 23
  outliers final: 15
  residues processed: 74
  average time/residue: 0.9724
  time to fit residues: 75.9162
Evaluate side-chains
  74 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
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  299 GLN
Chi-restraints excluded: chain E residue  307 LEU
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 D residue   30 VAL
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  108 MET
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 A residue  341 VAL
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  455 LEU
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:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0070
   chunk 62 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0060
   overall best weight:    0.4214

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.158562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.133295 restraints weight = 5881.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.02
r_work: 0.3529 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3426 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.3102

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= 0.104
  Angle     :  0.583   9.107   7009  Z= 0.305
  Chirality :  0.045   0.150    752
  Planarity :  0.005   0.046    905
  Dihedral  :  4.128  16.933    736
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.34 %
    Favored  : 80.96 %
  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: -0.81 (0.33), residues: 642
  helix: -2.25 (1.02), residues: 21
  sheet:  0.67 (0.33), residues: 260
  loop : -1.41 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D  60 
 PHE   0.008   0.001   PHE A 400 
 TYR   0.013   0.001   TYR E 210 
 ARG   0.002   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00218 (    1)
  link_NAG-ASN         : angle       1.38635 (    3)
  hydrogen bonds       : bond        0.03373 (  157)
  hydrogen bonds       : angle       5.20991 (  414)
  SS BOND              : bond        0.00461 (    8)
  SS BOND              : angle       2.75426 (   16)
  covalent geometry    : bond        0.00224 ( 5149)
  covalent geometry    : angle       0.56774 ( 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
  74 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.512 
Fit side-chains
REVERT: E  250 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8046 (pp30)
REVERT: E  398 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8098 (mt)
REVERT: D   68 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7452 (mptt)
REVERT: A  455 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7694 (tt)
  outliers start: 20
  outliers final: 13
  residues processed: 67
  average time/residue: 0.9745
  time to fit residues: 68.8522
Evaluate side-chains
  66 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  250 GLN
Chi-restraints excluded: chain E residue  307 LEU
Chi-restraints excluded: chain E residue  392 CYS
Chi-restraints excluded: chain E residue  398 ILE
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  108 MET
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 A residue  341 VAL
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3829 r_free = 0.3829 target = 0.156604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.131421 restraints weight = 6042.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.01
r_work: 0.3504 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3205

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= 0.140
  Angle     :  0.634   8.525   7009  Z= 0.333
  Chirality :  0.046   0.158    752
  Planarity :  0.005   0.051    905
  Dihedral  :  4.369  17.695    736
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 15.71 %
    Favored  : 80.59 %
  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: -0.87 (0.33), residues: 642
  helix: -2.27 (1.04), residues: 21
  sheet:  0.59 (0.32), residues: 275
  loop : -1.50 (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   0.009   0.001   PHE A 400 
 TYR   0.016   0.002   TYR E 210 
 ARG   0.002   0.000   ARG E 222 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00200 (    1)
  link_NAG-ASN         : angle       1.33102 (    3)
  hydrogen bonds       : bond        0.03921 (  157)
  hydrogen bonds       : angle       5.36103 (  414)
  SS BOND              : bond        0.00638 (    8)
  SS BOND              : angle       2.99228 (   16)
  covalent geometry    : bond        0.00319 ( 5149)
  covalent geometry    : angle       0.61824 ( 6990)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4251.78 seconds
wall clock time: 75 minutes 16.28 seconds (4516.28 seconds total)