Starting phenix.real_space_refine
on Sat May 10 16:24:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dm8_27530/05_2025/8dm8_27530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dm8_27530/05_2025/8dm8_27530.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dm8_27530/05_2025/8dm8_27530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dm8_27530/05_2025/8dm8_27530.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dm8_27530/05_2025/8dm8_27530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dm8_27530/05_2025/8dm8_27530.cif"
  }
  resolution = 2.68
  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=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4139      2.51       5
     N    1087      2.21       5
     O    1216      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6479
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1604
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "D"
      Number of atoms: 4833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 593, 4833
          Classifications: {'peptide': 593}
          Link IDs: {'PTRANS': 27, 'TRANS': 565}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.90, per 1000 atoms: 0.76
  Number of scatterers: 6479
  At special positions: 0
  Unit cell: (77, 86, 121, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1216      8.00
     N    1087      7.00
     C    4139      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " 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 A1301 " - " ASN A 343 "
      " NAG D 701 " - " ASN D  53 "
      " NAG D 702 " - " ASN D 546 "
  Time building additional restraints: 1.49
  Conformation dependent library (CDL) restraints added in 882.3 milliseconds
  

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1498

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 7 sheets defined
      56.5% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.909A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.409A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'D' and resid 21 through 52
      removed outlier: 3.502A  pdb=" N   GLN D  34 " --> pdb=" O   ASN D  30 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASP D  38 " --> pdb=" O   GLN D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 81
    Processing helix  chain 'D' and resid 82 through 83
      No H-bonds generated for 'chain 'D' and resid 82 through 83'
    Processing helix  chain 'D' and resid 84 through 88
      removed outlier: 3.739A  pdb=" N   GLU D  87 " --> pdb=" O   SER D  84 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE D  88 " --> pdb=" O   LEU D  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 84 through 88'
    Processing helix  chain 'D' and resid 90 through 101
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 3.670A  pdb=" N   SER D 106 " --> pdb=" O   SER D 103 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA D 107 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU D 108 " --> pdb=" O   SER D 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 103 through 108'
    Processing helix  chain 'D' and resid 109 through 128
    Processing helix  chain 'D' and resid 147 through 155
    Processing helix  chain 'D' and resid 157 through 193
      removed outlier: 5.033A  pdb=" N   GLN D 175 " --> pdb=" O   GLU D 171 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
      removed outlier: 3.698A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 218 through 232
      removed outlier: 3.709A  pdb=" N   LEU D 222 " --> pdb=" O   ASN D 218 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   GLU D 224 " --> pdb=" O   ASN D 220 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLU D 232 " --> pdb=" O   ARG D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 252
    Processing helix  chain 'D' and resid 275 through 279
      removed outlier: 3.613A  pdb=" N   TYR D 279 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 303 through 318
    Processing helix  chain 'D' and resid 324 through 331
      removed outlier: 3.525A  pdb=" N   TRP D 328 " --> pdb=" O   THR D 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.622A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 413
      removed outlier: 3.848A  pdb=" N   GLY D 405 " --> pdb=" O   HIS D 401 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA D 413 " --> pdb=" O   SER D 409 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.613A  pdb=" N   GLU D 435 " --> pdb=" O   ASP D 431 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 465
      removed outlier: 4.419A  pdb=" N   PHE D 452 " --> pdb=" O   GLY D 448 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 484
      removed outlier: 3.672A  pdb=" N   LYS D 476 " --> pdb=" O   GLN D 472 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLU D 479 " --> pdb=" O   LYS D 475 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 499 through 502
      removed outlier: 3.663A  pdb=" N   SER D 502 " --> pdb=" O   ASP D 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 499 through 502'
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 512 through 533
      removed outlier: 4.307A  pdb=" N   TYR D 516 " --> pdb=" O   PHE D 512 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   PHE D 523 " --> pdb=" O   THR D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 4.128A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
    Processing helix  chain 'D' and resid 581 through 588
    Processing helix  chain 'D' and resid 588 through 598
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 6.549A  pdb=" N   ALA A 435 " --> pdb=" O   PHE A 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 133
    Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 263
      removed outlier: 6.019A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 352
      removed outlier: 6.332A  pdb=" N   ASP D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)

    331 hydrogen bonds defined for protein.
    951 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: 1.82

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2071
        1.35 -     1.47: 1789
        1.47 -     1.60: 2744
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6662
  Sorted by residual:
  bond pdb=" CG  PRO A 330 "
       pdb=" CD  PRO A 330 "
    ideal  model  delta    sigma   weight residual
    1.503  1.589 -0.086 3.40e-02 8.65e+02 6.41e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.454 -0.048 2.00e-02 2.50e+03 5.88e+00
  bond pdb=" C1  NAG D 702 "
       pdb=" O5  NAG D 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.24e+00
  bond pdb=" CB  ASN A 439 "
       pdb=" CG  ASN A 439 "
    ideal  model  delta    sigma   weight residual
    1.516  1.468  0.048 2.50e-02 1.60e+03 3.64e+00
  bond pdb=" CB  VAL D 573 "
       pdb=" CG2 VAL D 573 "
    ideal  model  delta    sigma   weight residual
    1.521  1.458  0.063 3.30e-02 9.18e+02 3.60e+00
  ... (remaining 6657 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 8688
        2.10 -     4.19: 313
        4.19 -     6.29: 37
        6.29 -     8.38: 7
        8.38 -    10.48: 3
  Bond angle restraints: 9048
  Sorted by residual:
  angle pdb=" N   ALA A 372 "
        pdb=" CA  ALA A 372 "
        pdb=" C   ALA A 372 "
      ideal   model   delta    sigma   weight residual
     109.81  120.01  -10.20 2.21e+00 2.05e-01 2.13e+01
  angle pdb=" CA  CYS A 391 "
        pdb=" CB  CYS A 391 "
        pdb=" SG  CYS A 391 "
      ideal   model   delta    sigma   weight residual
     114.40  124.88  -10.48 2.30e+00 1.89e-01 2.07e+01
  angle pdb=" N   VAL D 364 "
        pdb=" CA  VAL D 364 "
        pdb=" C   VAL D 364 "
      ideal   model   delta    sigma   weight residual
     106.21  110.87   -4.66 1.07e+00 8.73e-01 1.90e+01
  angle pdb=" CA  PRO A 330 "
        pdb=" N   PRO A 330 "
        pdb=" CD  PRO A 330 "
      ideal   model   delta    sigma   weight residual
     112.00  105.96    6.04 1.40e+00 5.10e-01 1.86e+01
  angle pdb=" C   SER A 359 "
        pdb=" N   ASN A 360 "
        pdb=" CA  ASN A 360 "
      ideal   model   delta    sigma   weight residual
     122.07  126.87   -4.80 1.43e+00 4.89e-01 1.13e+01
  ... (remaining 9043 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 3594
       17.35 -    34.71: 323
       34.71 -    52.06: 46
       52.06 -    69.41: 14
       69.41 -    86.77: 6
  Dihedral angle restraints: 3983
    sinusoidal: 1650
      harmonic: 2333
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.15   37.85     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CA  CYS A 391 "
           pdb=" C   CYS A 391 "
           pdb=" N   PHE A 392 "
           pdb=" CA  PHE A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.73  -20.27     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CG  ARG D 245 "
           pdb=" CD  ARG D 245 "
           pdb=" NE  ARG D 245 "
           pdb=" CZ  ARG D 245 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.53  -44.53     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 3980 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 641
       0.051 -    0.103: 234
       0.103 -    0.154: 56
       0.154 -    0.205: 13
       0.205 -    0.257: 3
  Chirality restraints: 947
  Sorted by residual:
  chirality pdb=" CB  ILE D 291 "
            pdb=" CA  ILE D 291 "
            pdb=" CG1 ILE D 291 "
            pdb=" CG2 ILE D 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  THR A 333 "
            pdb=" CA  THR A 333 "
            pdb=" OG1 THR A 333 "
            pdb=" CG2 THR A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  ASN A 360 "
            pdb=" N   ASN A 360 "
            pdb=" C   ASN A 360 "
            pdb=" CB  ASN A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 944 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D  36 "   -0.020 2.00e-02 2.50e+03   3.99e-02 1.60e+01
        pdb=" C   ALA D  36 "    0.069 2.00e-02 2.50e+03
        pdb=" O   ALA D  36 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLU D  37 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D  31 "   -0.014 2.00e-02 2.50e+03   2.83e-02 7.98e+00
        pdb=" C   ASN D  31 "    0.049 2.00e-02 2.50e+03
        pdb=" O   ASN D  31 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   PHE D  32 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 499 "   -0.044 5.00e-02 4.00e+02   6.53e-02 6.82e+00
        pdb=" N   PRO D 500 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO D 500 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 500 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 1992
        2.82 -     3.34: 5892
        3.34 -     3.86: 11313
        3.86 -     4.38: 13110
        4.38 -     4.90: 22401
  Nonbonded interactions: 54708
  Sorted by model distance:
  nonbonded pdb=" O   ILE D 151 "
            pdb=" OG  SER D 155 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OH  TYR D 183 "
            pdb=" OD1 ASP D 509 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OH  TYR D 217 "
            pdb=" OD2 ASP D 225 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OG1 THR A 500 "
            pdb=" OH  TYR D  41 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.361 3.040
  ... (remaining 54703 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:             3.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.050
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
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      :  0.006   0.086   6671  Z= 0.270
  Angle     :  0.902  10.477   9069  Z= 0.500
  Chirality :  0.058   0.257    947
  Planarity :  0.007   0.065   1172
  Dihedral  : 13.496  86.766   2467
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  1.74 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.26), residues: 790
  helix: -0.44 (0.22), residues: 397
  sheet:  0.63 (0.64), residues: 53
  loop : -0.52 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 163 
 HIS   0.006   0.002   HIS A 505 
 PHE   0.024   0.003   PHE A 375 
 TYR   0.032   0.003   TYR D 385 
 ARG   0.008   0.001   ARG D 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00620 (    3)
  link_NAG-ASN         : angle       3.10303 (    9)
  hydrogen bonds       : bond        0.14393 (  309)
  hydrogen bonds       : angle       6.53863 (  951)
  SS BOND              : bond        0.00698 (    6)
  SS BOND              : angle       2.22262 (   12)
  covalent geometry    : bond        0.00621 ( 6662)
  covalent geometry    : angle       0.89375 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 157
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 ASN cc_start: 0.7958 (m-40) cc_final: 0.7610 (m-40)
REVERT: A  414 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8665 (mm-40)
REVERT: D  113 ASN cc_start: 0.8620 (t0) cc_final: 0.8359 (t0)
REVERT: D  145 GLU cc_start: 0.8438 (tp30) cc_final: 0.7852 (tp30)
REVERT: D  347 THR cc_start: 0.8692 (m) cc_final: 0.8432 (p)
REVERT: D  383 MET cc_start: 0.9163 (mtp) cc_final: 0.8842 (mtp)
REVERT: D  483 GLU cc_start: 0.8473 (tp30) cc_final: 0.8257 (tp30)
  outliers start: 5
  outliers final: 0
  residues processed: 161
  average time/residue: 1.3232
  time to fit residues: 222.4869
Evaluate side-chains
  95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
D  34 GLN
D 137 ASN
D 188 ASN
D 378 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.096513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.073092 restraints weight = 11732.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 2.60
r_work: 0.2805 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   6671  Z= 0.273
  Angle     :  0.661   8.635   9069  Z= 0.344
  Chirality :  0.047   0.191    947
  Planarity :  0.005   0.039   1172
  Dihedral  :  5.609  46.981    931
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 10.85 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.28), residues: 790
  helix:  0.50 (0.25), residues: 410
  sheet:  1.28 (0.76), residues: 43
  loop : -0.26 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 163 
 HIS   0.004   0.001   HIS D 493 
 PHE   0.014   0.002   PHE D  32 
 TYR   0.019   0.002   TYR A 396 
 ARG   0.009   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00447 (    3)
  link_NAG-ASN         : angle       2.40017 (    9)
  hydrogen bonds       : bond        0.05477 (  309)
  hydrogen bonds       : angle       4.94381 (  951)
  SS BOND              : bond        0.00608 (    6)
  SS BOND              : angle       1.30497 (   12)
  covalent geometry    : bond        0.00634 ( 6662)
  covalent geometry    : angle       0.65548 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8577 (mtmm)
REVERT: D  145 GLU cc_start: 0.8351 (tp30) cc_final: 0.7815 (tm-30)
REVERT: D  190 MET cc_start: 0.9037 (tmm) cc_final: 0.8757 (tmm)
REVERT: D  341 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8514 (mppt)
REVERT: D  347 THR cc_start: 0.8811 (m) cc_final: 0.8455 (p)
REVERT: D  383 MET cc_start: 0.9372 (mtp) cc_final: 0.9085 (mtp)
REVERT: D  483 GLU cc_start: 0.9035 (tp30) cc_final: 0.8643 (tp30)
  outliers start: 21
  outliers final: 7
  residues processed: 109
  average time/residue: 1.2523
  time to fit residues: 143.2176
Evaluate side-chains
  95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue   60 GLN
Chi-restraints excluded: chain D residue  320 LEU
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  334 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0570
   chunk 42 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 41 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
D 472 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.098107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.074650 restraints weight = 11792.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.63
r_work: 0.2850 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6671  Z= 0.160
  Angle     :  0.566   7.537   9069  Z= 0.292
  Chirality :  0.043   0.162    947
  Planarity :  0.004   0.040   1172
  Dihedral  :  5.049  48.150    931
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.02 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.29), residues: 790
  helix:  0.87 (0.25), residues: 410
  sheet:  1.35 (0.78), residues: 43
  loop : -0.04 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 241 
 PHE   0.013   0.001   PHE D 315 
 TYR   0.013   0.001   TYR D 385 
 ARG   0.008   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00310 (    3)
  link_NAG-ASN         : angle       2.05869 (    9)
  hydrogen bonds       : bond        0.04642 (  309)
  hydrogen bonds       : angle       4.67483 (  951)
  SS BOND              : bond        0.00469 (    6)
  SS BOND              : angle       1.25297 (   12)
  covalent geometry    : bond        0.00368 ( 6662)
  covalent geometry    : angle       0.56077 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: D  145 GLU cc_start: 0.8470 (tp30) cc_final: 0.7902 (tm-30)
REVERT: D  190 MET cc_start: 0.9040 (tmm) cc_final: 0.8725 (tmm)
REVERT: D  383 MET cc_start: 0.9357 (mtp) cc_final: 0.9025 (mtp)
REVERT: D  483 GLU cc_start: 0.8982 (tp30) cc_final: 0.8610 (tp30)
REVERT: D  597 GLU cc_start: 0.8739 (tp30) cc_final: 0.8282 (tt0)
REVERT: D  598 GLN cc_start: 0.8289 (mt0) cc_final: 0.8012 (mt0)
REVERT: D  603 PHE cc_start: 0.8478 (t80) cc_final: 0.8187 (t80)
  outliers start: 18
  outliers final: 10
  residues processed: 97
  average time/residue: 1.3687
  time to fit residues: 139.4449
Evaluate side-chains
  94 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  320 LEU
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  491 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0980
   chunk 60 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.095340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.070907 restraints weight = 11078.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.53
r_work: 0.2768 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6671  Z= 0.159
  Angle     :  0.621  15.420   9069  Z= 0.303
  Chirality :  0.044   0.224    947
  Planarity :  0.004   0.042   1172
  Dihedral  :  6.018  57.672    931
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.30 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.29), residues: 790
  helix:  1.08 (0.26), residues: 409
  sheet:  1.18 (0.77), residues: 43
  loop : -0.02 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.013   0.001   HIS A 519 
 PHE   0.013   0.001   PHE D 369 
 TYR   0.013   0.001   TYR D 385 
 ARG   0.006   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00341 (    3)
  link_NAG-ASN         : angle       6.89462 (    9)
  hydrogen bonds       : bond        0.04506 (  309)
  hydrogen bonds       : angle       4.62141 (  951)
  SS BOND              : bond        0.00440 (    6)
  SS BOND              : angle       1.14362 (   12)
  covalent geometry    : bond        0.00363 ( 6662)
  covalent geometry    : angle       0.58074 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: D   86 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8647 (mp10)
REVERT: D  145 GLU cc_start: 0.8462 (tp30) cc_final: 0.7892 (tm-30)
REVERT: D  383 MET cc_start: 0.9345 (mtp) cc_final: 0.9075 (mtp)
REVERT: D  483 GLU cc_start: 0.8992 (tp30) cc_final: 0.8585 (tp30)
REVERT: D  491 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8562 (pt)
REVERT: D  597 GLU cc_start: 0.8810 (tp30) cc_final: 0.8268 (tt0)
REVERT: D  598 GLN cc_start: 0.8300 (mt0) cc_final: 0.8041 (mt0)
REVERT: D  603 PHE cc_start: 0.8469 (t80) cc_final: 0.8230 (t80)
  outliers start: 21
  outliers final: 12
  residues processed: 94
  average time/residue: 1.2642
  time to fit residues: 124.8804
Evaluate side-chains
  93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  320 LEU
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  491 LEU
Chi-restraints excluded: chain D residue  506 VAL
Chi-restraints excluded: chain D residue  531 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0770
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    1.0742

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.095391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.071998 restraints weight = 11834.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 2.60
r_work: 0.2786 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6671  Z= 0.225
  Angle     :  0.625  11.503   9069  Z= 0.313
  Chirality :  0.045   0.182    947
  Planarity :  0.004   0.041   1172
  Dihedral  :  5.987  54.798    931
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 13.02 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.30), residues: 790
  helix:  1.13 (0.26), residues: 409
  sheet:  1.18 (0.76), residues: 43
  loop :  0.04 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 163 
 HIS   0.004   0.001   HIS D 241 
 PHE   0.013   0.001   PHE D 315 
 TYR   0.016   0.002   TYR D 385 
 ARG   0.007   0.001   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00506 (    3)
  link_NAG-ASN         : angle       5.52971 (    9)
  hydrogen bonds       : bond        0.04960 (  309)
  hydrogen bonds       : angle       4.72303 (  951)
  SS BOND              : bond        0.00522 (    6)
  SS BOND              : angle       1.18353 (   12)
  covalent geometry    : bond        0.00526 ( 6662)
  covalent geometry    : angle       0.59986 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   87 GLU cc_start: 0.8053 (pm20) cc_final: 0.7804 (pm20)
REVERT: D  145 GLU cc_start: 0.8463 (tp30) cc_final: 0.7891 (tm-30)
REVERT: D  190 MET cc_start: 0.8996 (tmm) cc_final: 0.8712 (tmm)
REVERT: D  383 MET cc_start: 0.9358 (mtp) cc_final: 0.9084 (mtp)
REVERT: D  483 GLU cc_start: 0.9035 (tp30) cc_final: 0.8631 (tp30)
REVERT: D  597 GLU cc_start: 0.8808 (tp30) cc_final: 0.8605 (tp30)
  outliers start: 20
  outliers final: 10
  residues processed: 93
  average time/residue: 1.2074
  time to fit residues: 118.1366
Evaluate side-chains
  88 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 ASP
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  320 LEU
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  491 LEU
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0970
   chunk 6 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.5578

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.095455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.070669 restraints weight = 11024.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 2.59
r_work: 0.2732 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2597 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6671  Z= 0.146
  Angle     :  0.582   9.938   9069  Z= 0.289
  Chirality :  0.043   0.158    947
  Planarity :  0.004   0.054   1172
  Dihedral  :  5.761  56.728    931
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.62 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.30), residues: 790
  helix:  1.37 (0.26), residues: 403
  sheet:  0.93 (0.77), residues: 44
  loop :  0.16 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 163 
 HIS   0.003   0.001   HIS D 241 
 PHE   0.014   0.001   PHE D 369 
 TYR   0.012   0.001   TYR D 385 
 ARG   0.011   0.001   ARG D 600 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00457 (    3)
  link_NAG-ASN         : angle       4.92335 (    9)
  hydrogen bonds       : bond        0.04411 (  309)
  hydrogen bonds       : angle       4.61380 (  951)
  SS BOND              : bond        0.00463 (    6)
  SS BOND              : angle       1.18619 (   12)
  covalent geometry    : bond        0.00333 ( 6662)
  covalent geometry    : angle       0.56008 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
REVERT: D   87 GLU cc_start: 0.8094 (pm20) cc_final: 0.7786 (pm20)
REVERT: D  114 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8314 (mmmm)
REVERT: D  145 GLU cc_start: 0.8429 (tp30) cc_final: 0.7888 (tm-30)
REVERT: D  190 MET cc_start: 0.8993 (tmm) cc_final: 0.8756 (tmm)
REVERT: D  360 MET cc_start: 0.8950 (ttm) cc_final: 0.8632 (ptm)
REVERT: D  383 MET cc_start: 0.9347 (mtp) cc_final: 0.9099 (mtp)
REVERT: D  483 GLU cc_start: 0.9041 (tp30) cc_final: 0.8683 (tp30)
REVERT: D  491 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8560 (pt)
  outliers start: 14
  outliers final: 9
  residues processed: 88
  average time/residue: 1.2560
  time to fit residues: 116.4107
Evaluate side-chains
  90 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  320 LEU
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  491 LEU
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.096676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.073205 restraints weight = 11764.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 2.62
r_work: 0.2807 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6671  Z= 0.182
  Angle     :  0.599   9.503   9069  Z= 0.299
  Chirality :  0.044   0.157    947
  Planarity :  0.004   0.040   1172
  Dihedral  :  5.691  54.769    931
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.34 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.30), residues: 790
  helix:  1.38 (0.26), residues: 403
  sheet:  0.95 (0.76), residues: 44
  loop :  0.15 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 163 
 HIS   0.003   0.001   HIS D 241 
 PHE   0.013   0.001   PHE D 369 
 TYR   0.014   0.001   TYR D 385 
 ARG   0.006   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00426 (    3)
  link_NAG-ASN         : angle       4.86144 (    9)
  hydrogen bonds       : bond        0.04614 (  309)
  hydrogen bonds       : angle       4.62527 (  951)
  SS BOND              : bond        0.00458 (    6)
  SS BOND              : angle       1.19143 (   12)
  covalent geometry    : bond        0.00422 ( 6662)
  covalent geometry    : angle       0.57789 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
REVERT: A  478 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8503 (mmmt)
REVERT: D   87 GLU cc_start: 0.8181 (pm20) cc_final: 0.7925 (pm20)
REVERT: D  114 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8359 (mmmm)
REVERT: D  145 GLU cc_start: 0.8458 (tp30) cc_final: 0.7914 (tm-30)
REVERT: D  163 TRP cc_start: 0.8169 (t60) cc_final: 0.7911 (t60)
REVERT: D  383 MET cc_start: 0.9339 (mtp) cc_final: 0.9104 (mtp)
REVERT: D  483 GLU cc_start: 0.9031 (tp30) cc_final: 0.8670 (tp30)
REVERT: D  491 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8549 (pt)
REVERT: D  597 GLU cc_start: 0.8670 (tp30) cc_final: 0.8260 (tt0)
REVERT: D  598 GLN cc_start: 0.8308 (mt0) cc_final: 0.8099 (mt0)
  outliers start: 12
  outliers final: 9
  residues processed: 87
  average time/residue: 1.3200
  time to fit residues: 120.5895
Evaluate side-chains
  93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  320 LEU
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  491 LEU
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.095101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.070132 restraints weight = 10997.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 2.61
r_work: 0.2727 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2591 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6671  Z= 0.165
  Angle     :  0.597   9.186   9069  Z= 0.298
  Chirality :  0.043   0.212    947
  Planarity :  0.004   0.057   1172
  Dihedral  :  5.653  55.706    931
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.05 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.30), residues: 790
  helix:  1.44 (0.26), residues: 403
  sheet:  0.99 (0.77), residues: 44
  loop :  0.14 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 163 
 HIS   0.003   0.001   HIS D 241 
 PHE   0.020   0.001   PHE D 603 
 TYR   0.013   0.001   TYR D 385 
 ARG   0.013   0.001   ARG D 600 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00407 (    3)
  link_NAG-ASN         : angle       4.69066 (    9)
  hydrogen bonds       : bond        0.04470 (  309)
  hydrogen bonds       : angle       4.59434 (  951)
  SS BOND              : bond        0.00446 (    6)
  SS BOND              : angle       1.21130 (   12)
  covalent geometry    : bond        0.00383 ( 6662)
  covalent geometry    : angle       0.57774 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8580 (ptm160)
REVERT: A  478 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8549 (mmmt)
REVERT: D   86 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8626 (mp10)
REVERT: D   87 GLU cc_start: 0.8167 (pm20) cc_final: 0.7875 (pm20)
REVERT: D  114 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8364 (mmmm)
REVERT: D  145 GLU cc_start: 0.8471 (tp30) cc_final: 0.7921 (tm-30)
REVERT: D  151 ILE cc_start: 0.8106 (mt) cc_final: 0.7844 (mt)
REVERT: D  163 TRP cc_start: 0.8109 (t60) cc_final: 0.7864 (t60)
REVERT: D  190 MET cc_start: 0.8995 (tmm) cc_final: 0.8722 (tmm)
REVERT: D  383 MET cc_start: 0.9344 (mtp) cc_final: 0.9114 (mtp)
REVERT: D  483 GLU cc_start: 0.9059 (tp30) cc_final: 0.8754 (tp30)
REVERT: D  491 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8562 (pt)
REVERT: D  597 GLU cc_start: 0.8765 (tp30) cc_final: 0.8247 (tt0)
REVERT: D  598 GLN cc_start: 0.8265 (mt0) cc_final: 0.8052 (mt0)
  outliers start: 15
  outliers final: 11
  residues processed: 92
  average time/residue: 1.3349
  time to fit residues: 128.7179
Evaluate side-chains
  98 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 ASP
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  320 LEU
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  491 LEU
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.096982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.073532 restraints weight = 11842.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.63
r_work: 0.2845 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6671  Z= 0.168
  Angle     :  0.598   9.125   9069  Z= 0.298
  Chirality :  0.044   0.200    947
  Planarity :  0.004   0.039   1172
  Dihedral  :  5.596  54.262    931
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.05 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.30), residues: 790
  helix:  1.45 (0.26), residues: 403
  sheet:  1.06 (0.76), residues: 44
  loop :  0.14 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 163 
 HIS   0.003   0.001   HIS D 241 
 PHE   0.018   0.001   PHE D 603 
 TYR   0.013   0.001   TYR D 385 
 ARG   0.006   0.001   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00394 (    3)
  link_NAG-ASN         : angle       4.67804 (    9)
  hydrogen bonds       : bond        0.04493 (  309)
  hydrogen bonds       : angle       4.59940 (  951)
  SS BOND              : bond        0.00459 (    6)
  SS BOND              : angle       1.20208 (   12)
  covalent geometry    : bond        0.00390 ( 6662)
  covalent geometry    : angle       0.57876 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8578 (ptm160)
REVERT: A  478 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8508 (mmmt)
REVERT: D   86 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8576 (mp10)
REVERT: D   87 GLU cc_start: 0.8147 (pm20) cc_final: 0.7859 (pm20)
REVERT: D  114 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8386 (mmmm)
REVERT: D  145 GLU cc_start: 0.8460 (tp30) cc_final: 0.7927 (tm-30)
REVERT: D  151 ILE cc_start: 0.8121 (mt) cc_final: 0.7860 (mt)
REVERT: D  163 TRP cc_start: 0.8172 (t60) cc_final: 0.7945 (t60)
REVERT: D  190 MET cc_start: 0.9023 (tmm) cc_final: 0.8782 (tmm)
REVERT: D  383 MET cc_start: 0.9337 (mtp) cc_final: 0.9104 (mtp)
REVERT: D  483 GLU cc_start: 0.9019 (tp30) cc_final: 0.8707 (tp30)
REVERT: D  491 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8567 (pt)
REVERT: D  597 GLU cc_start: 0.8855 (tp30) cc_final: 0.8299 (tt0)
  outliers start: 12
  outliers final: 10
  residues processed: 90
  average time/residue: 1.3916
  time to fit residues: 131.0938
Evaluate side-chains
  99 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  320 LEU
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  491 LEU
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 46 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    0.2980
   chunk 35 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
D 368 ASN
D 598 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.096170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.071311 restraints weight = 11040.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 2.64
r_work: 0.2743 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6671  Z= 0.136
  Angle     :  0.591   9.248   9069  Z= 0.294
  Chirality :  0.043   0.185    947
  Planarity :  0.004   0.068   1172
  Dihedral  :  5.530  55.831    931
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.34 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.30), residues: 790
  helix:  1.47 (0.26), residues: 402
  sheet:  1.07 (0.77), residues: 44
  loop :  0.17 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 163 
 HIS   0.003   0.001   HIS D 374 
 PHE   0.018   0.001   PHE D 603 
 TYR   0.012   0.001   TYR D 385 
 ARG   0.014   0.001   ARG D 600 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00344 (    3)
  link_NAG-ASN         : angle       4.58681 (    9)
  hydrogen bonds       : bond        0.04271 (  309)
  hydrogen bonds       : angle       4.54008 (  951)
  SS BOND              : bond        0.00461 (    6)
  SS BOND              : angle       1.21187 (   12)
  covalent geometry    : bond        0.00313 ( 6662)
  covalent geometry    : angle       0.57156 ( 9048)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8474 (ptm160)
REVERT: A  478 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8540 (mmmt)
REVERT: D   86 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8617 (mp10)
REVERT: D   87 GLU cc_start: 0.8160 (pm20) cc_final: 0.7875 (pm20)
REVERT: D  114 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8353 (mmmm)
REVERT: D  145 GLU cc_start: 0.8484 (tp30) cc_final: 0.7927 (tm-30)
REVERT: D  163 TRP cc_start: 0.8146 (t60) cc_final: 0.7915 (t60)
REVERT: D  190 MET cc_start: 0.8988 (tmm) cc_final: 0.8748 (tmm)
REVERT: D  383 MET cc_start: 0.9327 (mtp) cc_final: 0.9104 (mtp)
REVERT: D  483 GLU cc_start: 0.9062 (tp30) cc_final: 0.8759 (tp30)
REVERT: D  597 GLU cc_start: 0.8703 (tp30) cc_final: 0.8204 (tt0)
  outliers start: 13
  outliers final: 8
  residues processed: 90
  average time/residue: 1.3510
  time to fit residues: 128.2741
Evaluate side-chains
  95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  320 LEU
Chi-restraints excluded: chain D residue  334 THR
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 74 optimal weight:    0.1980
   chunk 78 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.096881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.073532 restraints weight = 12102.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.67
r_work: 0.2827 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6671  Z= 0.175
  Angle     :  0.605   9.261   9069  Z= 0.302
  Chirality :  0.044   0.186    947
  Planarity :  0.004   0.039   1172
  Dihedral  :  5.530  55.531    931
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.48 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.30), residues: 790
  helix:  1.46 (0.26), residues: 402
  sheet:  1.04 (0.77), residues: 44
  loop :  0.16 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 594 
 HIS   0.003   0.001   HIS D 241 
 PHE   0.018   0.001   PHE D 603 
 TYR   0.014   0.001   TYR D 385 
 ARG   0.005   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00376 (    3)
  link_NAG-ASN         : angle       4.66233 (    9)
  hydrogen bonds       : bond        0.04571 (  309)
  hydrogen bonds       : angle       4.58982 (  951)
  SS BOND              : bond        0.00462 (    6)
  SS BOND              : angle       1.20996 (   12)
  covalent geometry    : bond        0.00407 ( 6662)
  covalent geometry    : angle       0.58560 ( 9048)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5444.21 seconds
wall clock time: 95 minutes 7.30 seconds (5707.30 seconds total)