Starting phenix.real_space_refine
on Tue Mar  3 15:11:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fdk_31546/03_2026/7fdk_31546.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fdk_31546/03_2026/7fdk_31546.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fdk_31546/03_2026/7fdk_31546.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fdk_31546/03_2026/7fdk_31546.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fdk_31546/03_2026/7fdk_31546.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fdk_31546/03_2026/7fdk_31546.map"
  }
  resolution = 3.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.000 sd=   0.004
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    4113      2.51       5
     N    1076      2.21       5
     O    1223      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6449
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4867
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4860
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 26, 'TRANS': 570}
      Conformer: "B"
        Number of residues, atoms: 597, 4860
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 26, 'TRANS': 570}
          bond proxies already assigned to first conformer: 4986
    Chain: "E"
      Number of atoms: 1540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1540
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      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: 1.96, per 1000 atoms: 0.30
  Number of scatterers: 6449
  At special positions: 0
  Unit cell: (118.56, 83.2, 80.08, 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    1223      8.00
     N    1076      7.00
     C    4113      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 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 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  53 "
      " NAG E 601 " - " ASN E 343 "
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 361.9 milliseconds
  

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 6 sheets defined
      50.8% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.883A  pdb=" N   ASN A  24 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ASP A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 79
      removed outlier: 4.058A  pdb=" N   SER A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   GLU A  64 " --> pdb=" O   GLN A  60 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ALA A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A  66 " --> pdb=" O   MET A  62 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   THR A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 144 through 148
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 3.614A  pdb=" N   THR A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      Proline residue:  A 178  - end of helix
      removed outlier: 3.962A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 231
      removed outlier: 4.171A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.540A  pdb=" N   LYS A 247 " --> pdb=" O   TYR A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.561A  pdb=" N   THR A 282 " --> pdb=" O   TYR A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 299
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.526A  pdb=" N   ALA A 311 " --> pdb=" O   ILE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.808A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ALA A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.248A  pdb=" N   ALA A 372 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 411
      removed outlier: 4.328A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 465
      removed outlier: 4.036A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LEU A 450 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      removed outlier: 3.549A  pdb=" N   ARG A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 485
    Processing helix  chain 'A' and resid 499 through 503
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.439A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 4.528A  pdb=" N   LEU A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.529A  pdb=" N   ALA A 569 " --> pdb=" O   PRO A 565 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'E' and resid 337 through 343
    Processing helix  chain 'E' and resid 365 through 370
    Processing helix  chain 'E' and resid 383 through 390
    Processing helix  chain 'E' and resid 403 through 407
      removed outlier: 3.638A  pdb=" N   GLU E 406 " --> pdb=" O   ARG E 403 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 438 through 443
      removed outlier: 3.524A  pdb=" N   ASP E 442 " --> pdb=" O   SER E 438 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.405A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.426A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 355
      removed outlier: 4.005A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU E 516 " --> pdb=" O   ASN E 394 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE E 402 " --> pdb=" O   TYR E 508 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474

    270 hydrogen bonds defined for protein.
    788 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: 0.84

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2071
        1.34 -     1.46: 1721
        1.46 -     1.58: 2781
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6631
  Sorted by residual:
  bond pdb=" C   LYS A 359 "
       pdb=" N   MET A 360 "
    ideal  model  delta    sigma   weight residual
    1.330  1.535 -0.205 1.23e-02 6.61e+03 2.79e+02
  bond pdb=" C   ILE A 358 "
       pdb=" N   LYS A 359 "
    ideal  model  delta    sigma   weight residual
    1.331  1.551 -0.221 1.66e-02 3.63e+03 1.77e+02
  bond pdb=" C   ALA E 397 "
       pdb=" N   ASP E 398 "
    ideal  model  delta    sigma   weight residual
    1.328  1.432 -0.104 1.42e-02 4.96e+03 5.37e+01
  bond pdb=" C   ASP E 398 "
       pdb=" N   SER E 399 "
    ideal  model  delta    sigma   weight residual
    1.332  1.392 -0.060 1.25e-02 6.40e+03 2.34e+01
  bond pdb=" C   SER A 563 "
       pdb=" N   GLU A 564 "
    ideal  model  delta    sigma   weight residual
    1.335  1.231  0.104 3.04e-02 1.08e+03 1.16e+01
  ... (remaining 6626 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 8756
        2.24 -     4.47: 219
        4.47 -     6.71: 29
        6.71 -     8.95: 2
        8.95 -    11.18: 4
  Bond angle restraints: 9010
  Sorted by residual:
  angle pdb=" O   ILE A 358 "
        pdb=" C   ILE A 358 "
        pdb=" N   LYS A 359 "
      ideal   model   delta    sigma   weight residual
     123.26  134.44  -11.18 1.08e+00 8.57e-01 1.07e+02
  angle pdb=" CA  ILE A 358 "
        pdb=" C   ILE A 358 "
        pdb=" N   LYS A 359 "
      ideal   model   delta    sigma   weight residual
     116.31  105.62   10.69 1.14e+00 7.69e-01 8.79e+01
  angle pdb=" N   GLN A  86 "
        pdb=" CA  GLN A  86 "
        pdb=" C   GLN A  86 "
      ideal   model   delta    sigma   weight residual
     114.56  108.10    6.46 1.27e+00 6.20e-01 2.59e+01
  angle pdb=" O   ALA E 397 "
        pdb=" C   ALA E 397 "
        pdb=" N   ASP E 398 "
      ideal   model   delta    sigma   weight residual
     123.27  129.19   -5.92 1.17e+00 7.31e-01 2.56e+01
  angle pdb=" CA  ALA E 397 "
        pdb=" C   ALA E 397 "
        pdb=" N   ASP E 398 "
      ideal   model   delta    sigma   weight residual
     116.45  110.39    6.06 1.23e+00 6.61e-01 2.43e+01
  ... (remaining 9005 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 3478
       17.73 -    35.45: 361
       35.45 -    53.18: 74
       53.18 -    70.91: 18
       70.91 -    88.64: 10
  Dihedral angle restraints: 3941
    sinusoidal: 1615
      harmonic: 2326
  Sorted by residual:
  dihedral pdb=" CA  GLU A 145 "
           pdb=" C   GLU A 145 "
           pdb=" N   PRO A 146 "
           pdb=" CA  PRO A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.48  -49.52     0      5.00e+00 4.00e-02 9.81e+01
  dihedral pdb=" CA  VAL A 581 "
           pdb=" C   VAL A 581 "
           pdb=" N   LYS A 582 "
           pdb=" CA  LYS A 582 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.16   29.84     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  CYS E 361 "
           pdb=" C   CYS E 361 "
           pdb=" N   VAL E 362 "
           pdb=" CA  VAL E 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.67   28.33     0      5.00e+00 4.00e-02 3.21e+01
  ... (remaining 3938 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 523
       0.036 -    0.072: 311
       0.072 -    0.108: 84
       0.108 -    0.144: 22
       0.144 -    0.180: 4
  Chirality restraints: 944
  Sorted by residual:
  chirality pdb=" C1  NAG E 601 "
            pdb=" ND2 ASN E 343 "
            pdb=" C2  NAG E 601 "
            pdb=" O5  NAG E 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.11e-01
  chirality pdb=" CA  PRO E 337 "
            pdb=" N   PRO E 337 "
            pdb=" C   PRO E 337 "
            pdb=" CB  PRO E 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.60e-01
  chirality pdb=" CA  ILE E 434 "
            pdb=" N   ILE E 434 "
            pdb=" C   ILE E 434 "
            pdb=" CB  ILE E 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.57e-01
  ... (remaining 941 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 145 "   -0.046 5.00e-02 4.00e+02   6.91e-02 7.64e+00
        pdb=" N   PRO A 146 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 453 "    0.021 2.00e-02 2.50e+03   1.68e-02 5.68e+00
        pdb=" CG  TYR E 453 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 453 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 453 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 453 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 453 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 453 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR E 453 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 388 "   -0.039 5.00e-02 4.00e+02   5.78e-02 5.35e+00
        pdb=" N   PRO A 389 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 389 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 389 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 138
        2.64 -     3.21: 6520
        3.21 -     3.77: 9963
        3.77 -     4.34: 13424
        4.34 -     4.90: 21531
  Nonbonded interactions: 51576
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" O   THR E 500 "
     model   vdw
     2.080 3.040
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" O   VAL A 485 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OH  TYR A 535 "
            pdb=" O   SER A 538 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" O   ILE E 418 "
            pdb=" N   ASP E 420 "
     model   vdw
     2.122 3.120
  nonbonded pdb=" OH  TYR A 535 "
            pdb=" O   LYS A 541 "
     model   vdw
     2.156 3.040
  ... (remaining 51571 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.540
  Find NCS groups from input model:        0.030
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
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      :  0.008   0.221   6637  Z= 0.439
  Angle     :  0.889  11.185   9025  Z= 0.523
  Chirality :  0.048   0.180    944
  Planarity :  0.006   0.069   1167
  Dihedral  : 15.522  88.637   2442
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 18.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 13.21 %
    Favored  : 86.66 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  6.83 %
    Favored  : 92.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.54 (0.24), residues: 788
  helix: -2.30 (0.21), residues: 373
  sheet: -3.02 (0.68), residues: 44
  loop : -3.82 (0.27), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 454 
 TYR   0.041   0.002   TYR E 453 
 PHE   0.028   0.003   PHE A 390 
 TRP   0.028   0.002   TRP A 302 
 HIS   0.006   0.002   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00848 ( 6631)
  covalent geometry    : angle       0.88154 ( 9010)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       2.12552 (    6)
  hydrogen bonds       : bond        0.16363 (  270)
  hydrogen bonds       : angle       7.44417 (  788)
  link_NAG-ASN         : bond        0.00919 (    3)
  link_NAG-ASN         : angle       3.36865 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 HIS cc_start: 0.8167 (p-80) cc_final: 0.7876 (p90)
REVERT: A  297 MET cc_start: 0.6037 (ptt) cc_final: 0.5796 (ptp)
REVERT: A  454 TYR cc_start: 0.7576 (t80) cc_final: 0.7248 (t80)
REVERT: E  346 ARG cc_start: 0.7135 (ttm110) cc_final: 0.5726 (ptt180)
REVERT: E  356 LYS cc_start: 0.8944 (tttm) cc_final: 0.8681 (ttmt)
REVERT: E  357 ARG cc_start: 0.8591 (ttt90) cc_final: 0.6565 (mtt180)
REVERT: E  424 LYS cc_start: 0.8907 (tptp) cc_final: 0.8506 (tttp)
REVERT: E  451 TYR cc_start: 0.8043 (m-80) cc_final: 0.7096 (m-80)
REVERT: E  462 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8407 (mtpp)
REVERT: E  465 GLU cc_start: 0.6059 (tp30) cc_final: 0.5740 (tp30)
REVERT: E  466 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8212 (ttm110)
REVERT: E  467 ASP cc_start: 0.7996 (t0) cc_final: 0.7492 (t70)
REVERT: E  508 TYR cc_start: 0.8344 (m-80) cc_final: 0.7998 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 99
  average time/residue: 0.1078
  time to fit residues: 13.4832
Evaluate side-chains
  77 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A  33 ASN
A  34 GLN
A 134 ASN
A 195 ASN
A 388 GLN
A 522 GLN
A 599 ASN
E 460 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.140623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.111542 restraints weight = 20491.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.115300 restraints weight = 13865.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.115606 restraints weight = 9364.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.116423 restraints weight = 5909.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.118952 restraints weight = 5224.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3610 r_free = 0.3610    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3610 r_free = 0.3610    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6637  Z= 0.172
  Angle     :  0.689   8.240   9025  Z= 0.351
  Chirality :  0.044   0.220    944
  Planarity :  0.006   0.062   1167
  Dihedral  :  7.072  58.632    932
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.66 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.34 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.27), residues: 788
  helix: -0.71 (0.25), residues: 370
  sheet: -2.78 (0.64), residues: 50
  loop : -3.25 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 408 
 TYR   0.017   0.002   TYR E 453 
 PHE   0.018   0.002   PHE A 390 
 TRP   0.023   0.002   TRP A 163 
 HIS   0.004   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 6631)
  covalent geometry    : angle       0.68273 ( 9010)
  SS BOND              : bond        0.00145 (    3)
  SS BOND              : angle       1.88660 (    6)
  hydrogen bonds       : bond        0.04907 (  270)
  hydrogen bonds       : angle       5.38844 (  788)
  link_NAG-ASN         : bond        0.00611 (    3)
  link_NAG-ASN         : angle       2.56627 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.6815 (mtp) cc_final: 0.6574 (ttm)
REVERT: A  265 HIS cc_start: 0.8085 (p-80) cc_final: 0.7683 (p90)
REVERT: A  383 MET cc_start: 0.8739 (ttt) cc_final: 0.8434 (ttt)
REVERT: A  557 MET cc_start: 0.8896 (tmm) cc_final: 0.8653 (tmm)
REVERT: E  347 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6272 (m-80)
REVERT: E  357 ARG cc_start: 0.8556 (ttt90) cc_final: 0.6473 (mtt180)
REVERT: E  424 LYS cc_start: 0.8854 (tptp) cc_final: 0.8441 (tttp)
REVERT: E  451 TYR cc_start: 0.8018 (m-80) cc_final: 0.6875 (m-80)
REVERT: E  462 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8385 (mtpp)
REVERT: E  467 ASP cc_start: 0.7738 (t0) cc_final: 0.7153 (t70)
REVERT: E  495 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8071 (p90)
REVERT: E  508 TYR cc_start: 0.8314 (m-80) cc_final: 0.7867 (m-80)
  outliers start: 9
  outliers final: 5
  residues processed: 98
  average time/residue: 0.0957
  time to fit residues: 12.1139
Evaluate side-chains
  84 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0970
   chunk 62 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.143858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.114175 restraints weight = 13544.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.114981 restraints weight = 7210.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.115926 restraints weight = 6349.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.116444 restraints weight = 4907.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.116706 restraints weight = 4789.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6637  Z= 0.140
  Angle     :  0.644   7.896   9025  Z= 0.325
  Chirality :  0.043   0.205    944
  Planarity :  0.005   0.058   1167
  Dihedral  :  6.414  56.499    932
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.64 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.23 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.29), residues: 788
  helix: -0.00 (0.27), residues: 369
  sheet: -2.24 (0.66), residues: 50
  loop : -2.74 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 408 
 TYR   0.023   0.002   TYR A 252 
 PHE   0.016   0.002   PHE A 390 
 TRP   0.020   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6631)
  covalent geometry    : angle       0.63859 ( 9010)
  SS BOND              : bond        0.00128 (    3)
  SS BOND              : angle       1.58153 (    6)
  hydrogen bonds       : bond        0.04472 (  270)
  hydrogen bonds       : angle       5.01459 (  788)
  link_NAG-ASN         : bond        0.00478 (    3)
  link_NAG-ASN         : angle       2.41838 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 GLN cc_start: 0.6633 (mm-40) cc_final: 0.6419 (pp30)
REVERT: A  265 HIS cc_start: 0.7912 (p-80) cc_final: 0.7435 (p90)
REVERT: A  402 GLU cc_start: 0.6913 (tp30) cc_final: 0.6475 (mp0)
REVERT: A  591 LEU cc_start: 0.8199 (tt) cc_final: 0.7865 (mt)
REVERT: E  347 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6228 (m-80)
REVERT: E  356 LYS cc_start: 0.8688 (tttt) cc_final: 0.7722 (mmtt)
REVERT: E  357 ARG cc_start: 0.8586 (ttt90) cc_final: 0.6448 (mtt180)
REVERT: E  424 LYS cc_start: 0.8722 (tptp) cc_final: 0.8340 (tttm)
REVERT: E  451 TYR cc_start: 0.7899 (m-80) cc_final: 0.6954 (m-80)
REVERT: E  462 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8334 (mtpp)
REVERT: E  467 ASP cc_start: 0.7798 (t0) cc_final: 0.7419 (t70)
REVERT: E  495 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.8095 (p90)
REVERT: E  508 TYR cc_start: 0.8430 (m-80) cc_final: 0.8083 (m-80)
  outliers start: 12
  outliers final: 7
  residues processed: 110
  average time/residue: 0.0917
  time to fit residues: 13.3241
Evaluate side-chains
  94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0670
   chunk 46 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 41 optimal weight:   20.0000
   chunk 77 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    2.0522

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.141793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.110752 restraints weight = 14361.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.113583 restraints weight = 8273.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.114554 restraints weight = 5749.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.114743 restraints weight = 4785.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.114765 restraints weight = 4687.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3564
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6637  Z= 0.180
  Angle     :  0.677   7.885   9025  Z= 0.338
  Chirality :  0.044   0.201    944
  Planarity :  0.005   0.056   1167
  Dihedral  :  6.146  56.802    932
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.28 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.10 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.86 (0.29), residues: 788
  helix:  0.05 (0.27), residues: 379
  sheet: -2.04 (0.69), residues: 46
  loop : -2.59 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.019   0.002   TYR A 454 
 PHE   0.019   0.002   PHE A 390 
 TRP   0.018   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 6631)
  covalent geometry    : angle       0.67082 ( 9010)
  SS BOND              : bond        0.00140 (    3)
  SS BOND              : angle       1.86110 (    6)
  hydrogen bonds       : bond        0.04533 (  270)
  hydrogen bonds       : angle       4.99060 (  788)
  link_NAG-ASN         : bond        0.00516 (    3)
  link_NAG-ASN         : angle       2.49608 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLN cc_start: 0.6534 (mm-40) cc_final: 0.6290 (pp30)
REVERT: A  249 MET cc_start: 0.8442 (ttm) cc_final: 0.8035 (tpp)
REVERT: A  265 HIS cc_start: 0.8017 (p-80) cc_final: 0.7576 (p90)
REVERT: A  402 GLU cc_start: 0.7070 (tp30) cc_final: 0.6609 (mp0)
REVERT: E  347 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6125 (m-80)
REVERT: E  356 LYS cc_start: 0.8653 (tttt) cc_final: 0.7693 (mmtt)
REVERT: E  357 ARG cc_start: 0.8600 (ttt90) cc_final: 0.6533 (mtt180)
REVERT: E  424 LYS cc_start: 0.8780 (tptp) cc_final: 0.8480 (tttp)
REVERT: E  451 TYR cc_start: 0.7932 (m-80) cc_final: 0.7055 (m-80)
REVERT: E  462 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8386 (mtpp)
REVERT: E  495 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8243 (p90)
REVERT: E  508 TYR cc_start: 0.8456 (m-80) cc_final: 0.8129 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 100
  average time/residue: 0.0899
  time to fit residues: 12.0368
Evaluate side-chains
  94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 72 optimal weight:    0.0050
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0470
   chunk 7 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.4092

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

Flipped N/Q/H residues before XYZ refinement:
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.148302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.118433 restraints weight = 13620.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.120292 restraints weight = 7100.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.121112 restraints weight = 5773.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.121523 restraints weight = 4513.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.121799 restraints weight = 4488.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3665 r_free = 0.3665    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3665 r_free = 0.3665    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3665
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6637  Z= 0.117
  Angle     :  0.615   7.179   9025  Z= 0.307
  Chirality :  0.041   0.193    944
  Planarity :  0.005   0.055   1167
  Dihedral  :  5.365  55.326    932
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.50 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.55 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.30), residues: 788
  helix:  0.46 (0.27), residues: 380
  sheet: -1.67 (0.69), residues: 46
  loop : -2.34 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 466 
 TYR   0.018   0.001   TYR A 587 
 PHE   0.013   0.001   PHE A 525 
 TRP   0.019   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6631)
  covalent geometry    : angle       0.61081 ( 9010)
  SS BOND              : bond        0.00108 (    3)
  SS BOND              : angle       1.63883 (    6)
  hydrogen bonds       : bond        0.03827 (  270)
  hydrogen bonds       : angle       4.75259 (  788)
  link_NAG-ASN         : bond        0.00403 (    3)
  link_NAG-ASN         : angle       2.03232 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.8429 (ttm) cc_final: 0.8107 (tpp)
REVERT: A  265 HIS cc_start: 0.8051 (p-80) cc_final: 0.7745 (p90)
REVERT: A  267 LEU cc_start: 0.8342 (mt) cc_final: 0.7728 (mt)
REVERT: A  270 MET cc_start: 0.5945 (tpp) cc_final: 0.5504 (tpp)
REVERT: A  401 HIS cc_start: 0.7586 (OUTLIER) cc_final: 0.6767 (m-70)
REVERT: A  402 GLU cc_start: 0.6969 (tp30) cc_final: 0.6560 (mp0)
REVERT: A  480 MET cc_start: 0.8044 (mtp) cc_final: 0.7667 (mtm)
REVERT: E  356 LYS cc_start: 0.8583 (tttt) cc_final: 0.7866 (mmtt)
REVERT: E  357 ARG cc_start: 0.8508 (ttt90) cc_final: 0.6350 (mtt180)
REVERT: E  424 LYS cc_start: 0.8630 (tptp) cc_final: 0.8290 (tttm)
REVERT: E  451 TYR cc_start: 0.7751 (m-80) cc_final: 0.6779 (m-80)
REVERT: E  462 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8150 (mtpp)
REVERT: E  467 ASP cc_start: 0.7711 (t0) cc_final: 0.7378 (t70)
REVERT: E  468 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8734 (mt)
REVERT: E  508 TYR cc_start: 0.8388 (m-80) cc_final: 0.8103 (m-80)
REVERT: E  515 PHE cc_start: 0.7091 (m-80) cc_final: 0.6759 (m-80)
REVERT: E  516 GLU cc_start: 0.6797 (pm20) cc_final: 0.6442 (pm20)
  outliers start: 14
  outliers final: 8
  residues processed: 114
  average time/residue: 0.1037
  time to fit residues: 15.3803
Evaluate side-chains
  104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 56 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.142849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.112936 restraints weight = 11474.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.112606 restraints weight = 7306.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.114172 restraints weight = 6175.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.114125 restraints weight = 5183.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.114203 restraints weight = 4752.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6637  Z= 0.217
  Angle     :  0.708   8.558   9025  Z= 0.352
  Chirality :  0.045   0.199    944
  Planarity :  0.005   0.053   1167
  Dihedral  :  5.811  56.306    932
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.53 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.57 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.30), residues: 788
  helix:  0.30 (0.27), residues: 379
  sheet: -1.62 (0.72), residues: 46
  loop : -2.39 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 408 
 TYR   0.021   0.002   TYR E 453 
 PHE   0.023   0.002   PHE A 390 
 TRP   0.015   0.002   TRP A 163 
 HIS   0.007   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 6631)
  covalent geometry    : angle       0.70301 ( 9010)
  SS BOND              : bond        0.00202 (    3)
  SS BOND              : angle       1.77501 (    6)
  hydrogen bonds       : bond        0.04585 (  270)
  hydrogen bonds       : angle       4.92289 (  788)
  link_NAG-ASN         : bond        0.00569 (    3)
  link_NAG-ASN         : angle       2.50942 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7307 (mt)
REVERT: A  265 HIS cc_start: 0.8050 (p-80) cc_final: 0.7800 (p90)
REVERT: A  267 LEU cc_start: 0.8363 (mt) cc_final: 0.7688 (mt)
REVERT: A  402 GLU cc_start: 0.7150 (tp30) cc_final: 0.6718 (mp0)
REVERT: E  347 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6370 (m-80)
REVERT: E  356 LYS cc_start: 0.8563 (tttt) cc_final: 0.7646 (mmtt)
REVERT: E  357 ARG cc_start: 0.8618 (ttt90) cc_final: 0.6591 (mtt180)
REVERT: E  451 TYR cc_start: 0.7921 (m-80) cc_final: 0.7101 (m-80)
REVERT: E  462 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8358 (mtpp)
REVERT: E  495 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8096 (p90)
REVERT: E  508 TYR cc_start: 0.8420 (m-80) cc_final: 0.8132 (m-80)
  outliers start: 16
  outliers final: 11
  residues processed: 93
  average time/residue: 0.1046
  time to fit residues: 12.6305
Evaluate side-chains
  91 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 62 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 586 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.148260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.118858 restraints weight = 13811.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.117175 restraints weight = 7760.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.118258 restraints weight = 6615.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.118694 restraints weight = 5746.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.119604 restraints weight = 5090.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3633 r_free = 0.3633    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.3328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6637  Z= 0.122
  Angle     :  0.630   7.728   9025  Z= 0.310
  Chirality :  0.042   0.198    944
  Planarity :  0.005   0.052   1167
  Dihedral  :  5.395  55.365    932
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.15 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.30), residues: 788
  helix:  0.55 (0.27), residues: 379
  sheet: -1.32 (0.72), residues: 46
  loop : -2.16 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 466 
 TYR   0.020   0.001   TYR A  50 
 PHE   0.012   0.001   PHE A 390 
 TRP   0.017   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6631)
  covalent geometry    : angle       0.62603 ( 9010)
  SS BOND              : bond        0.00109 (    3)
  SS BOND              : angle       1.69845 (    6)
  hydrogen bonds       : bond        0.03864 (  270)
  hydrogen bonds       : angle       4.69871 (  788)
  link_NAG-ASN         : bond        0.00418 (    3)
  link_NAG-ASN         : angle       2.02356 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  161 ARG cc_start: 0.7044 (mtp180) cc_final: 0.6500 (ttt180)
REVERT: A  168 TRP cc_start: 0.7450 (t-100) cc_final: 0.6907 (t-100)
REVERT: A  249 MET cc_start: 0.8349 (ttm) cc_final: 0.7834 (tpp)
REVERT: A  265 HIS cc_start: 0.8074 (p-80) cc_final: 0.7239 (p90)
REVERT: A  267 LEU cc_start: 0.8375 (mt) cc_final: 0.7696 (mt)
REVERT: A  383 MET cc_start: 0.8614 (ttt) cc_final: 0.8391 (ttt)
REVERT: A  402 GLU cc_start: 0.6727 (tp30) cc_final: 0.6355 (mp0)
REVERT: A  480 MET cc_start: 0.8014 (mtp) cc_final: 0.7617 (mtm)
REVERT: A  557 MET cc_start: 0.8734 (tmm) cc_final: 0.8503 (tmm)
REVERT: A  591 LEU cc_start: 0.8185 (tt) cc_final: 0.7860 (tt)
REVERT: E  355 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7993 (ttm-80)
REVERT: E  356 LYS cc_start: 0.8550 (tttt) cc_final: 0.7732 (mmtt)
REVERT: E  357 ARG cc_start: 0.8587 (ttt90) cc_final: 0.6501 (mtt180)
REVERT: E  451 TYR cc_start: 0.7749 (m-80) cc_final: 0.6885 (m-80)
REVERT: E  462 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8249 (mtpp)
REVERT: E  474 GLN cc_start: 0.7244 (tt0) cc_final: 0.6850 (pm20)
REVERT: E  495 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7940 (p90)
REVERT: E  508 TYR cc_start: 0.8426 (m-80) cc_final: 0.8105 (m-80)
REVERT: E  516 GLU cc_start: 0.6903 (pm20) cc_final: 0.6512 (pm20)
  outliers start: 11
  outliers final: 9
  residues processed: 94
  average time/residue: 0.1075
  time to fit residues: 13.0269
Evaluate side-chains
  94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 76 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS    B
** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.141200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.110890 restraints weight = 12415.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.109782 restraints weight = 7947.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.111358 restraints weight = 6291.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.111566 restraints weight = 5160.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.111946 restraints weight = 5002.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3530
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3530 r_free = 0.3530    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   6637  Z= 0.266
  Angle     :  0.748   8.795   9025  Z= 0.374
  Chirality :  0.046   0.207    944
  Planarity :  0.005   0.052   1167
  Dihedral  :  6.020  56.669    932
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.53 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.57 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.30), residues: 788
  helix:  0.29 (0.27), residues: 377
  sheet: -1.41 (0.75), residues: 48
  loop : -2.29 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 466 
 TYR   0.023   0.002   TYR E 453 
 PHE   0.027   0.002   PHE A 390 
 TRP   0.014   0.002   TRP A 163 
 HIS   0.008   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 ( 6631)
  covalent geometry    : angle       0.74144 ( 9010)
  SS BOND              : bond        0.00270 (    3)
  SS BOND              : angle       1.99171 (    6)
  hydrogen bonds       : bond        0.04854 (  270)
  hydrogen bonds       : angle       4.98896 (  788)
  link_NAG-ASN         : bond        0.00693 (    3)
  link_NAG-ASN         : angle       2.71119 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7379 (mt)
REVERT: A  249 MET cc_start: 0.8428 (ttm) cc_final: 0.7871 (tpp)
REVERT: A  265 HIS cc_start: 0.8096 (p-80) cc_final: 0.7637 (p90)
REVERT: A  267 LEU cc_start: 0.8414 (mt) cc_final: 0.7746 (mt)
REVERT: A  270 MET cc_start: 0.5817 (tpp) cc_final: 0.5066 (tpp)
REVERT: A  402 GLU cc_start: 0.6995 (tp30) cc_final: 0.6465 (mp0)
REVERT: A  489 GLU cc_start: 0.6142 (pt0) cc_final: 0.5864 (pt0)
REVERT: A  557 MET cc_start: 0.8801 (tmm) cc_final: 0.8590 (tmm)
REVERT: E  346 ARG cc_start: 0.7185 (ttm110) cc_final: 0.5715 (ptt180)
REVERT: E  347 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6340 (m-80)
REVERT: E  357 ARG cc_start: 0.8719 (ttt90) cc_final: 0.6669 (mtt180)
REVERT: E  451 TYR cc_start: 0.8031 (m-80) cc_final: 0.7209 (m-80)
REVERT: E  462 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8368 (mtpp)
REVERT: E  495 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8021 (p90)
REVERT: E  508 TYR cc_start: 0.8433 (m-80) cc_final: 0.8139 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 85
  average time/residue: 0.1000
  time to fit residues: 11.1054
Evaluate side-chains
  88 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  347 PHE
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  468 ILE
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0170
   chunk 9 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
E 409 GLN
** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.148233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.117121 restraints weight = 13902.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.120357 restraints weight = 7852.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.120955 restraints weight = 5483.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.121118 restraints weight = 4585.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.121469 restraints weight = 4208.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3665 r_free = 0.3665    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3665 r_free = 0.3665    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3665
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6637  Z= 0.128
  Angle     :  0.646   7.642   9025  Z= 0.321
  Chirality :  0.042   0.199    944
  Planarity :  0.005   0.051   1167
  Dihedral  :  5.393  55.339    932
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.75 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 18.02 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.30), residues: 788
  helix:  0.55 (0.27), residues: 378
  sheet: -1.21 (0.75), residues: 46
  loop : -2.09 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 466 
 TYR   0.016   0.001   TYR A 587 
 PHE   0.011   0.001   PHE A 512 
 TRP   0.018   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6631)
  covalent geometry    : angle       0.64122 ( 9010)
  SS BOND              : bond        0.00135 (    3)
  SS BOND              : angle       1.67850 (    6)
  hydrogen bonds       : bond        0.03897 (  270)
  hydrogen bonds       : angle       4.71738 (  788)
  link_NAG-ASN         : bond        0.00439 (    3)
  link_NAG-ASN         : angle       2.12276 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7304 (mt)
REVERT: A  161 ARG cc_start: 0.7255 (mtp180) cc_final: 0.6500 (mtp180)
REVERT: A  249 MET cc_start: 0.8237 (ttm) cc_final: 0.7875 (tpp)
REVERT: A  265 HIS cc_start: 0.7949 (p-80) cc_final: 0.7446 (p90)
REVERT: A  267 LEU cc_start: 0.8290 (mt) cc_final: 0.7788 (mt)
REVERT: A  402 GLU cc_start: 0.6633 (tp30) cc_final: 0.6231 (mp0)
REVERT: A  410 LEU cc_start: 0.8305 (mt) cc_final: 0.7995 (tp)
REVERT: A  591 LEU cc_start: 0.8196 (tt) cc_final: 0.7860 (tt)
REVERT: E  346 ARG cc_start: 0.7102 (ttm110) cc_final: 0.5517 (ptt180)
REVERT: E  356 LYS cc_start: 0.8413 (tttt) cc_final: 0.7575 (mmtt)
REVERT: E  357 ARG cc_start: 0.8584 (ttt90) cc_final: 0.6551 (mtt180)
REVERT: E  451 TYR cc_start: 0.7733 (m-80) cc_final: 0.6940 (m-80)
REVERT: E  454 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.8024 (ttm-80)
REVERT: E  462 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8275 (mtpp)
REVERT: E  474 GLN cc_start: 0.7350 (tt0) cc_final: 0.6910 (pm20)
REVERT: E  495 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7956 (p90)
REVERT: E  508 TYR cc_start: 0.8389 (m-80) cc_final: 0.8085 (m-80)
  outliers start: 11
  outliers final: 6
  residues processed: 91
  average time/residue: 0.1055
  time to fit residues: 12.3732
Evaluate side-chains
  89 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  501 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.148276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.116821 restraints weight = 14288.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.119240 restraints weight = 8035.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.120078 restraints weight = 6285.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.120238 restraints weight = 5154.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.120660 restraints weight = 4636.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   6637  Z= 0.136
  Angle     :  0.657   7.775   9025  Z= 0.326
  Chirality :  0.042   0.195    944
  Planarity :  0.005   0.052   1167
  Dihedral  :  5.181  55.552    930
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.64 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.02 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.31), residues: 788
  helix:  0.71 (0.28), residues: 371
  sheet: -1.02 (0.76), residues: 46
  loop : -2.09 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 466 
 TYR   0.015   0.001   TYR A 587 
 PHE   0.015   0.001   PHE A 390 
 TRP   0.016   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6631)
  covalent geometry    : angle       0.65221 ( 9010)
  SS BOND              : bond        0.00106 (    3)
  SS BOND              : angle       1.67511 (    6)
  hydrogen bonds       : bond        0.03911 (  270)
  hydrogen bonds       : angle       4.68591 (  788)
  link_NAG-ASN         : bond        0.00426 (    3)
  link_NAG-ASN         : angle       2.14474 (    9)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7324 (mt)
REVERT: A  249 MET cc_start: 0.8223 (ttm) cc_final: 0.7862 (tpp)
REVERT: A  267 LEU cc_start: 0.8261 (mt) cc_final: 0.7619 (mt)
REVERT: A  402 GLU cc_start: 0.6746 (tp30) cc_final: 0.6348 (mp0)
REVERT: A  410 LEU cc_start: 0.8244 (mt) cc_final: 0.8022 (tp)
REVERT: A  557 MET cc_start: 0.8742 (tmm) cc_final: 0.8507 (tmm)
REVERT: A  591 LEU cc_start: 0.8208 (tt) cc_final: 0.7857 (tt)
REVERT: E  346 ARG cc_start: 0.7076 (ttm110) cc_final: 0.5481 (ptt180)
REVERT: E  356 LYS cc_start: 0.8446 (tttt) cc_final: 0.7641 (mmtt)
REVERT: E  357 ARG cc_start: 0.8572 (ttt90) cc_final: 0.6565 (mtt180)
REVERT: E  451 TYR cc_start: 0.7836 (m-80) cc_final: 0.6983 (m-80)
REVERT: E  462 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8219 (mtpp)
REVERT: E  474 GLN cc_start: 0.7366 (tt0) cc_final: 0.6882 (pm20)
REVERT: E  495 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7879 (p90)
REVERT: E  508 TYR cc_start: 0.8364 (m-80) cc_final: 0.8068 (m-80)
  outliers start: 14
  outliers final: 9
  residues processed: 95
  average time/residue: 0.1050
  time to fit residues: 12.8808
Evaluate side-chains
  91 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain E residue  398 ASP
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  478 THR
Chi-restraints excluded: chain E residue  495 TYR
Chi-restraints excluded: chain E residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 28 optimal weight:    0.2980
   chunk 5 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0030
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.151127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.120462 restraints weight = 22175.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.123739 restraints weight = 14406.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.124300 restraints weight = 10214.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.127930 restraints weight = 6607.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.128053 restraints weight = 4681.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6637  Z= 0.124
  Angle     :  0.657   8.027   9025  Z= 0.325
  Chirality :  0.042   0.195    944
  Planarity :  0.005   0.051   1167
  Dihedral  :  5.043  54.806    930
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.19 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.31), residues: 788
  helix:  0.73 (0.27), residues: 373
  sheet: -1.03 (0.75), residues: 46
  loop : -2.02 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 466 
 TYR   0.016   0.001   TYR A 587 
 PHE   0.015   0.001   PHE A 512 
 TRP   0.070   0.002   TRP A 168 
 HIS   0.006   0.001   HIS E 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6631)
  covalent geometry    : angle       0.65325 ( 9010)
  SS BOND              : bond        0.00115 (    3)
  SS BOND              : angle       1.58069 (    6)
  hydrogen bonds       : bond        0.03697 (  270)
  hydrogen bonds       : angle       4.66569 (  788)
  link_NAG-ASN         : bond        0.00402 (    3)
  link_NAG-ASN         : angle       1.97320 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1306.16 seconds
wall clock time: 23 minutes 11.35 seconds (1391.35 seconds total)