Starting phenix.real_space_refine
on Thu Jul 24 17:20:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yf2_39208/07_2025/8yf2_39208.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yf2_39208/07_2025/8yf2_39208.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yf2_39208/07_2025/8yf2_39208.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yf2_39208/07_2025/8yf2_39208.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yf2_39208/07_2025/8yf2_39208.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yf2_39208/07_2025/8yf2_39208.cif"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      36      5.16       5
     C    4159      2.51       5
     N    1066      2.21       5
     O    1242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6504
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 1537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1537
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "A"
      Number of atoms: 4840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4840
          Classifications: {'peptide': 589}
          Link IDs: {'PTRANS': 27, 'TRANS': 561}
          Chain breaks: 1
    Chain: "C"
      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: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      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: "F"
      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: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {' ZN': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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: 8.23, per 1000 atoms: 1.27
  Number of scatterers: 6504
  At special positions: 0
  Unit cell: (75.9, 96.6, 126.27, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      36     16.00
     O    1242      8.00
     N    1066      7.00
     C    4159      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.07
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 702 " - " ASN A  53 "
      " NAG C   1 " - " ASN B 343 "
      " NAG D   1 " - " ASN A 216 "
      " NAG E   1 " - " ASN A 322 "
      " NAG F   1 " - " ASN A 299 "
  Time building additional restraints: 1.81
  Conformation dependent library (CDL) restraints added in 974.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 378 "


  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1476

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 5 sheets defined
      53.8% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.719A  pdb=" N   TYR B 369 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 365 through 370'
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 4.334A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
      removed outlier: 3.700A  pdb=" N   ASP B 420 " --> pdb=" O   GLY B 416 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   TYR B 421 " --> pdb=" O   LYS B 417 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASN B 422 " --> pdb=" O   ILE B 418 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 416 through 422'
    Processing helix  chain 'B' and resid 502 through 506
    Processing helix  chain 'A' and resid 22 through 54
      removed outlier: 3.892A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 5.077A  pdb=" N   GLU A  38 " --> pdb=" O   TYR A  34 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 80
      removed outlier: 4.471A  pdb=" N   GLN A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LYS A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 91 through 101
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 4.152A  pdb=" N   ASP A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 174
      removed outlier: 3.622A  pdb=" N   ALA A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 194
      removed outlier: 3.758A  pdb=" N   ALA A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASN A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 205 through 208
    Processing helix  chain 'A' and resid 219 through 231
      removed outlier: 4.412A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ASP A 224 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.506A  pdb=" N   THR A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   MET A 249 " --> pdb=" O   ARG A 245 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   ASP A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   THR A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.827A  pdb=" N   TYR A 279 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 299
    Processing helix  chain 'A' and resid 303 through 317
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.929A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.863A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A 384 " --> pdb=" O   GLN A 380 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.517A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 3.582A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE A 407 " --> pdb=" O   ALA A 403 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 472 through 485
      removed outlier: 3.577A  pdb=" N   THR A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.722A  pdb=" N   THR A 517 " --> pdb=" O   ILE A 513 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.516A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.956A  pdb=" N   GLU A 556 " --> pdb=" O   GLN A 552 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.891A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 598
      removed outlier: 3.867A  pdb=" N   GLU A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN A 598 " --> pdb=" O   TRP A 594 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.610A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.308A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350
      removed outlier: 3.524A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)

    273 hydrogen bonds defined for protein.
    777 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 2.15 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: 2057
        1.34 -     1.46: 1716
        1.46 -     1.58: 2858
        1.58 -     1.70: 0
        1.70 -     1.82: 57
  Bond restraints: 6688
  Sorted by residual:
  bond pdb=" N   ALA A 132 "
       pdb=" CA  ALA A 132 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.23e-02 6.61e+03 7.90e+00
  bond pdb=" CA  ALA A 242 "
       pdb=" CB  ALA A 242 "
    ideal  model  delta    sigma   weight residual
    1.532  1.494  0.039 1.79e-02 3.12e+03 4.64e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.38e+00
  bond pdb=" N   CYS A 133 "
       pdb=" CA  CYS A 133 "
    ideal  model  delta    sigma   weight residual
    1.458  1.497 -0.039 1.90e-02 2.77e+03 4.31e+00
  bond pdb=" N   GLU A 536 "
       pdb=" CA  GLU A 536 "
    ideal  model  delta    sigma   weight residual
    1.455  1.478 -0.023 1.23e-02 6.61e+03 3.36e+00
  ... (remaining 6683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 8875
        1.81 -     3.61: 182
        3.61 -     5.41: 29
        5.41 -     7.22: 2
        7.22 -     9.02: 1
  Bond angle restraints: 9089
  Sorted by residual:
  angle pdb=" C   CYS B 391 "
        pdb=" CA  CYS B 391 "
        pdb=" CB  CYS B 391 "
      ideal   model   delta    sigma   weight residual
     110.36  101.34    9.02 1.78e+00 3.16e-01 2.57e+01
  angle pdb=" N   VAL A 244 "
        pdb=" CA  VAL A 244 "
        pdb=" C   VAL A 244 "
      ideal   model   delta    sigma   weight residual
     110.53  106.20    4.33 9.40e-01 1.13e+00 2.13e+01
  angle pdb=" N   TYR A 243 "
        pdb=" CA  TYR A 243 "
        pdb=" C   TYR A 243 "
      ideal   model   delta    sigma   weight residual
     112.90  106.99    5.91 1.31e+00 5.83e-01 2.04e+01
  angle pdb=" N   PHE B 338 "
        pdb=" CA  PHE B 338 "
        pdb=" C   PHE B 338 "
      ideal   model   delta    sigma   weight residual
     112.72  107.25    5.47 1.36e+00 5.41e-01 1.62e+01
  angle pdb=" CA  ALA A 132 "
        pdb=" C   ALA A 132 "
        pdb=" O   ALA A 132 "
      ideal   model   delta    sigma   weight residual
     121.11  117.13    3.98 1.13e+00 7.83e-01 1.24e+01
  ... (remaining 9084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 3666
       17.15 -    34.30: 311
       34.30 -    51.44: 60
       51.44 -    68.59: 9
       68.59 -    85.74: 7
  Dihedral angle restraints: 4053
    sinusoidal: 1751
      harmonic: 2302
  Sorted by residual:
  dihedral pdb=" CA  PRO B 337 "
           pdb=" C   PRO B 337 "
           pdb=" N   PHE B 338 "
           pdb=" CA  PHE B 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.76   29.24     0      5.00e+00 4.00e-02 3.42e+01
  dihedral pdb=" CA  CYS B 525 "
           pdb=" C   CYS B 525 "
           pdb=" N   GLY B 526 "
           pdb=" CA  GLY B 526 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.43  -23.57     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" C   CYS B 391 "
           pdb=" N   CYS B 391 "
           pdb=" CA  CYS B 391 "
           pdb=" CB  CYS B 391 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.43  -11.17     0      2.50e+00 1.60e-01 2.00e+01
  ... (remaining 4050 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.184: 968
       0.184 -    0.369: 1
       0.369 -    0.553: 0
       0.553 -    0.737: 0
       0.737 -    0.922: 1
  Chirality restraints: 970
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 299 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.48   -0.92 2.00e-01 2.50e+01 2.12e+01
  chirality pdb=" CA  CYS B 391 "
            pdb=" N   CYS B 391 "
            pdb=" C   CYS B 391 "
            pdb=" CB  CYS B 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.37   -0.03 2.00e-02 2.50e+03 1.62e+00
  ... (remaining 967 not shown)

  Planarity restraints: 1166
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "   -0.330 2.00e-02 2.50e+03   2.86e-01 1.02e+03
        pdb=" C7  NAG F   1 "    0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "   -0.115 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "    0.512 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "   -0.141 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   2 "    0.101 2.00e-02 2.50e+03   8.33e-02 8.68e+01
        pdb=" C7  NAG F   2 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8  NAG F   2 "    0.076 2.00e-02 2.50e+03
        pdb=" N2  NAG F   2 "   -0.134 2.00e-02 2.50e+03
        pdb=" O7  NAG F   2 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 499 "   -0.026 5.00e-02 4.00e+02   4.01e-02 2.57e+00
        pdb=" N   PRO A 500 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1163 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1604
        2.79 -     3.32: 5615
        3.32 -     3.85: 9972
        3.85 -     4.37: 11601
        4.37 -     4.90: 20234
  Nonbonded interactions: 49026
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 217 "
            pdb=" OD2 ASP A 225 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" NH1 ARG A 177 "
            pdb=" O   GLU A 495 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" OD2 ASP B 442 "
            pdb=" OH  TYR B 451 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OG1 THR B 500 "
            pdb=" OH  TYR A  41 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG1 THR A 365 "
            pdb=" OD1 ASP A 367 "
     model   vdw
     2.376 3.040
  ... (remaining 49021 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             15.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     25.560
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:16.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   58.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
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      :  0.004   0.047   6705  Z= 0.183
  Angle     :  0.657  11.567   9128  Z= 0.354
  Chirality :  0.054   0.922    970
  Planarity :  0.010   0.286   1161
  Dihedral  : 13.039  85.738   2559
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.47 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.31), residues: 777
  helix:  1.03 (0.29), residues: 353
  sheet:  3.00 (0.77), residues: 44
  loop : -1.34 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.009   0.001   PHE A 438 
 TYR   0.014   0.001   TYR B 473 
 ARG   0.003   0.000   ARG A  95 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01130 (    5)
  link_NAG-ASN         : angle       4.38578 (   15)
  link_BETA1-4         : bond        0.02383 (    4)
  link_BETA1-4         : angle       3.85645 (   12)
  hydrogen bonds       : bond        0.20075 (  273)
  hydrogen bonds       : angle       5.32615 (  777)
  metal coordination   : bond        0.00070 (    2)
  SS BOND              : bond        0.01569 (    6)
  SS BOND              : angle       2.64434 (   12)
  covalent geometry    : bond        0.00342 ( 6688)
  covalent geometry    : angle       0.61094 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  465 GLU cc_start: 0.7644 (tt0) cc_final: 0.7439 (tt0)
  outliers start: 1
  outliers final: 2
  residues processed: 88
  average time/residue: 1.8762
  time to fit residues: 171.0034
Evaluate side-chains
  46 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  532 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 58 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
A 524 GLN
A 535 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.059572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.047011 restraints weight = 25889.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 3.99
r_work: 0.2834 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6705  Z= 0.137
  Angle     :  0.621   9.205   9128  Z= 0.314
  Chirality :  0.044   0.270    970
  Planarity :  0.004   0.036   1161
  Dihedral  :  7.598  56.187   1050
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.86 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  7.83 %
    Favored  : 90.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.31), residues: 777
  helix:  1.18 (0.28), residues: 372
  sheet:  2.97 (0.75), residues: 44
  loop : -1.21 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 566 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.008   0.001   PHE B 400 
 TYR   0.010   0.001   TYR A  50 
 ARG   0.004   0.000   ARG A 600 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00619 (    5)
  link_NAG-ASN         : angle       3.13196 (   15)
  link_BETA1-4         : bond        0.00545 (    4)
  link_BETA1-4         : angle       2.12528 (   12)
  hydrogen bonds       : bond        0.05375 (  273)
  hydrogen bonds       : angle       4.09649 (  777)
  metal coordination   : bond        0.00105 (    2)
  SS BOND              : bond        0.00332 (    6)
  SS BOND              : angle       0.93209 (   12)
  covalent geometry    : bond        0.00309 ( 6688)
  covalent geometry    : angle       0.60351 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8988 (mt-10)
REVERT: A  480 MET cc_start: 0.9620 (OUTLIER) cc_final: 0.9196 (mtp)
  outliers start: 12
  outliers final: 1
  residues processed: 48
  average time/residue: 1.3569
  time to fit residues: 68.6213
Evaluate side-chains
  39 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain A residue  480 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0980
   chunk 41 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 76 optimal weight:    6.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN
** A 524 GLN ** 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 = 0.3283 r_free = 0.3283 target = 0.057956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.045201 restraints weight = 26621.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 4.07
r_work: 0.2781 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6705  Z= 0.183
  Angle     :  0.608   8.221   9128  Z= 0.304
  Chirality :  0.044   0.280    970
  Planarity :  0.004   0.036   1161
  Dihedral  :  6.821  53.225   1045
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.35 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.14 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.31), residues: 777
  helix:  1.41 (0.28), residues: 377
  sheet:  2.91 (0.75), residues: 45
  loop : -1.25 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.009   0.001   PHE A 308 
 TYR   0.011   0.001   TYR A  34 
 ARG   0.002   0.000   ARG A 600 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00792 (    5)
  link_NAG-ASN         : angle       3.38909 (   15)
  link_BETA1-4         : bond        0.00162 (    4)
  link_BETA1-4         : angle       1.87434 (   12)
  hydrogen bonds       : bond        0.05279 (  273)
  hydrogen bonds       : angle       3.91623 (  777)
  metal coordination   : bond        0.00080 (    2)
  SS BOND              : bond        0.00249 (    6)
  SS BOND              : angle       1.06050 (   12)
  covalent geometry    : bond        0.00428 ( 6688)
  covalent geometry    : angle       0.58871 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.776 
Fit side-chains
REVERT: B  516 GLU cc_start: 0.8618 (tt0) cc_final: 0.8206 (tm-30)
REVERT: A   30 GLU cc_start: 0.9246 (mm-30) cc_final: 0.9021 (mt-10)
REVERT: A  480 MET cc_start: 0.9606 (OUTLIER) cc_final: 0.9202 (mtp)
  outliers start: 6
  outliers final: 0
  residues processed: 43
  average time/residue: 1.6602
  time to fit residues: 75.0480
Evaluate side-chains
  34 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  480 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.3265 r_free = 0.3265 target = 0.057229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.044555 restraints weight = 26756.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 4.05
r_work: 0.2765 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6705  Z= 0.182
  Angle     :  0.601   8.419   9128  Z= 0.300
  Chirality :  0.044   0.257    970
  Planarity :  0.003   0.036   1161
  Dihedral  :  6.551  53.156   1045
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.22 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.30 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.31), residues: 777
  helix:  1.54 (0.28), residues: 380
  sheet:  2.63 (0.74), residues: 45
  loop : -1.25 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.009   0.001   PHE A 308 
 TYR   0.011   0.001   TYR A  34 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00749 (    5)
  link_NAG-ASN         : angle       3.38358 (   15)
  link_BETA1-4         : bond        0.00169 (    4)
  link_BETA1-4         : angle       1.86884 (   12)
  hydrogen bonds       : bond        0.05121 (  273)
  hydrogen bonds       : angle       3.87680 (  777)
  metal coordination   : bond        0.00137 (    2)
  SS BOND              : bond        0.00285 (    6)
  SS BOND              : angle       1.15791 (   12)
  covalent geometry    : bond        0.00429 ( 6688)
  covalent geometry    : angle       0.58046 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
REVERT: B  465 GLU cc_start: 0.8884 (tt0) cc_final: 0.8602 (mt-10)
REVERT: B  516 GLU cc_start: 0.8619 (tt0) cc_final: 0.8298 (tm-30)
REVERT: A   30 GLU cc_start: 0.9243 (mm-30) cc_final: 0.9013 (mt-10)
REVERT: A  480 MET cc_start: 0.9585 (OUTLIER) cc_final: 0.9187 (mtp)
  outliers start: 6
  outliers final: 1
  residues processed: 43
  average time/residue: 1.5277
  time to fit residues: 69.1895
Evaluate side-chains
  38 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain A residue  480 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 70 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 ASN
** A 524 GLN ** 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 = 0.3198 r_free = 0.3198 target = 0.054407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.041599 restraints weight = 27416.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 4.03
r_work: 0.2678 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8957
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.103   6705  Z= 0.361
  Angle     :  0.747   9.007   9128  Z= 0.377
  Chirality :  0.049   0.263    970
  Planarity :  0.004   0.045   1161
  Dihedral  :  6.728  51.945   1045
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.63 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 13.33 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.31), residues: 777
  helix:  1.45 (0.28), residues: 380
  sheet:  1.84 (0.74), residues: 50
  loop : -1.36 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.013   0.002   PHE A 230 
 TYR   0.019   0.002   TYR A  34 
 ARG   0.003   0.001   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00826 (    5)
  link_NAG-ASN         : angle       3.94698 (   15)
  link_BETA1-4         : bond        0.00280 (    4)
  link_BETA1-4         : angle       1.86402 (   12)
  hydrogen bonds       : bond        0.06835 (  273)
  hydrogen bonds       : angle       4.37274 (  777)
  metal coordination   : bond        0.00263 (    2)
  SS BOND              : bond        0.00506 (    6)
  SS BOND              : angle       1.97727 (   12)
  covalent geometry    : bond        0.00842 ( 6688)
  covalent geometry    : angle       0.72431 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.737 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8715 (mp0)
REVERT: B  462 LYS cc_start: 0.9170 (mtpt) cc_final: 0.8885 (mtmp)
REVERT: B  465 GLU cc_start: 0.8875 (tt0) cc_final: 0.8511 (mt-10)
REVERT: A  480 MET cc_start: 0.9559 (OUTLIER) cc_final: 0.9202 (mtp)
  outliers start: 6
  outliers final: 2
  residues processed: 39
  average time/residue: 1.3716
  time to fit residues: 56.7462
Evaluate side-chains
  34 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain A residue  480 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.3244 r_free = 0.3244 target = 0.056314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.043572 restraints weight = 26623.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 4.04
r_work: 0.2739 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6705  Z= 0.133
  Angle     :  0.614  10.056   9128  Z= 0.300
  Chirality :  0.043   0.248    970
  Planarity :  0.003   0.037   1161
  Dihedral  :  6.299  53.121   1045
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.35 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 14.64 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.31), residues: 777
  helix:  1.78 (0.28), residues: 374
  sheet:  2.30 (0.76), residues: 45
  loop : -1.24 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 308 
 TYR   0.011   0.001   TYR A 516 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00779 (    5)
  link_NAG-ASN         : angle       3.61042 (   15)
  link_BETA1-4         : bond        0.00291 (    4)
  link_BETA1-4         : angle       1.89846 (   12)
  hydrogen bonds       : bond        0.04925 (  273)
  hydrogen bonds       : angle       3.86027 (  777)
  metal coordination   : bond        0.00106 (    2)
  SS BOND              : bond        0.00244 (    6)
  SS BOND              : angle       1.09184 (   12)
  covalent geometry    : bond        0.00308 ( 6688)
  covalent geometry    : angle       0.59178 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.695 
Fit side-chains
REVERT: B  462 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8927 (mtmp)
REVERT: B  465 GLU cc_start: 0.8770 (tt0) cc_final: 0.8514 (mt-10)
REVERT: B  516 GLU cc_start: 0.8608 (tt0) cc_final: 0.8379 (tm-30)
REVERT: A   30 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8984 (mt-10)
REVERT: A  416 ASN cc_start: 0.9031 (m-40) cc_final: 0.8802 (t0)
REVERT: A  480 MET cc_start: 0.9561 (mtm) cc_final: 0.9177 (mtp)
  outliers start: 4
  outliers final: 2
  residues processed: 40
  average time/residue: 1.2925
  time to fit residues: 54.8443
Evaluate side-chains
  35 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain A residue  572 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0570
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.6106

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.3232 r_free = 0.3232 target = 0.055817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.043201 restraints weight = 26762.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 4.01
r_work: 0.2725 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8913
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   6705  Z= 0.195
  Angle     :  0.630  11.028   9128  Z= 0.310
  Chirality :  0.044   0.231    970
  Planarity :  0.004   0.037   1161
  Dihedral  :  6.176  52.395   1045
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.73 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 14.64 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.31), residues: 777
  helix:  1.86 (0.28), residues: 368
  sheet:  2.36 (0.77), residues: 45
  loop : -1.15 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.009   0.001   PHE A 523 
 TYR   0.020   0.001   TYR B 369 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00733 (    5)
  link_NAG-ASN         : angle       3.70969 (   15)
  link_BETA1-4         : bond        0.00183 (    4)
  link_BETA1-4         : angle       1.86269 (   12)
  hydrogen bonds       : bond        0.05193 (  273)
  hydrogen bonds       : angle       3.90205 (  777)
  metal coordination   : bond        0.00172 (    2)
  SS BOND              : bond        0.00248 (    6)
  SS BOND              : angle       1.28221 (   12)
  covalent geometry    : bond        0.00459 ( 6688)
  covalent geometry    : angle       0.60790 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.727 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8697 (mp0)
REVERT: B  462 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8889 (mtmp)
REVERT: B  465 GLU cc_start: 0.8829 (tt0) cc_final: 0.8543 (tt0)
REVERT: B  516 GLU cc_start: 0.8637 (tt0) cc_final: 0.8402 (tm-30)
REVERT: A   30 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8864 (mm-30)
REVERT: A  480 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9166 (mtp)
  outliers start: 5
  outliers final: 3
  residues processed: 38
  average time/residue: 1.3198
  time to fit residues: 53.3922
Evaluate side-chains
  37 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain A residue  480 MET
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 48 optimal weight:    0.1980
   chunk 32 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.3259 r_free = 0.3259 target = 0.056950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.044260 restraints weight = 26569.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 4.05
r_work: 0.2760 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6705  Z= 0.113
  Angle     :  0.588  11.484   9128  Z= 0.284
  Chirality :  0.042   0.227    970
  Planarity :  0.003   0.037   1161
  Dihedral  :  5.909  52.959   1045
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.09 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 14.64 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.31), residues: 777
  helix:  1.97 (0.29), residues: 369
  sheet:  2.37 (0.77), residues: 45
  loop : -1.06 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.006   0.001   PHE A 308 
 TYR   0.011   0.001   TYR A 516 
 ARG   0.001   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00792 (    5)
  link_NAG-ASN         : angle       3.64284 (   15)
  link_BETA1-4         : bond        0.00337 (    4)
  link_BETA1-4         : angle       1.87195 (   12)
  hydrogen bonds       : bond        0.04266 (  273)
  hydrogen bonds       : angle       3.67302 (  777)
  metal coordination   : bond        0.00091 (    2)
  SS BOND              : bond        0.00667 (    6)
  SS BOND              : angle       1.03061 (   12)
  covalent geometry    : bond        0.00261 ( 6688)
  covalent geometry    : angle       0.56522 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.604 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8701 (mp0)
REVERT: B  462 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8890 (mtmp)
REVERT: B  465 GLU cc_start: 0.8769 (tt0) cc_final: 0.8480 (tt0)
REVERT: A  416 ASN cc_start: 0.9018 (m-40) cc_final: 0.8811 (t0)
REVERT: A  480 MET cc_start: 0.9559 (OUTLIER) cc_final: 0.9180 (mtp)
  outliers start: 4
  outliers final: 3
  residues processed: 40
  average time/residue: 1.4907
  time to fit residues: 63.0428
Evaluate side-chains
  37 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain A residue  480 MET
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** 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 = 0.3197 r_free = 0.3197 target = 0.054474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.041668 restraints weight = 27686.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.2820 rms_B_bonded: 4.05
r_work: 0.2683 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.081   6705  Z= 0.298
  Angle     :  0.721  12.202   9128  Z= 0.356
  Chirality :  0.047   0.217    970
  Planarity :  0.004   0.041   1161
  Dihedral  :  6.212  51.660   1045
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.89 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 14.64 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.31), residues: 777
  helix:  1.77 (0.28), residues: 373
  sheet:  1.86 (0.76), residues: 50
  loop : -1.20 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.011   0.002   PHE A 308 
 TYR   0.018   0.002   TYR A  34 
 ARG   0.003   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00748 (    5)
  link_NAG-ASN         : angle       4.00262 (   15)
  link_BETA1-4         : bond        0.00205 (    4)
  link_BETA1-4         : angle       1.86931 (   12)
  hydrogen bonds       : bond        0.06119 (  273)
  hydrogen bonds       : angle       4.09543 (  777)
  metal coordination   : bond        0.00156 (    2)
  SS BOND              : bond        0.00492 (    6)
  SS BOND              : angle       1.90486 (   12)
  covalent geometry    : bond        0.00696 ( 6688)
  covalent geometry    : angle       0.69691 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.901 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8653 (mp0)
REVERT: A  480 MET cc_start: 0.9563 (OUTLIER) cc_final: 0.9239 (mtp)
  outliers start: 8
  outliers final: 3
  residues processed: 34
  average time/residue: 2.4361
  time to fit residues: 87.6878
Evaluate side-chains
  32 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain A residue  480 MET
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    0.2980
   chunk 12 optimal weight:    0.0050
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.3258 r_free = 0.3258 target = 0.056925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.044297 restraints weight = 27120.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 4.07
r_work: 0.2754 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6705  Z= 0.114
  Angle     :  0.636  12.162   9128  Z= 0.305
  Chirality :  0.042   0.227    970
  Planarity :  0.003   0.041   1161
  Dihedral  :  5.824  53.243   1045
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.47 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 15.07 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.31), residues: 777
  helix:  1.95 (0.28), residues: 369
  sheet:  2.31 (0.78), residues: 45
  loop : -1.03 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 566 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.009   0.001   PHE A 315 
 TYR   0.013   0.001   TYR A 516 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00827 (    5)
  link_NAG-ASN         : angle       3.82074 (   15)
  link_BETA1-4         : bond        0.00400 (    4)
  link_BETA1-4         : angle       1.88674 (   12)
  hydrogen bonds       : bond        0.04236 (  273)
  hydrogen bonds       : angle       3.65844 (  777)
  metal coordination   : bond        0.00080 (    2)
  SS BOND              : bond        0.00252 (    6)
  SS BOND              : angle       0.93115 (   12)
  covalent geometry    : bond        0.00260 ( 6688)
  covalent geometry    : angle       0.61355 ( 9089)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.685 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8729 (mp0)
REVERT: B  465 GLU cc_start: 0.8684 (tt0) cc_final: 0.8431 (mt-10)
REVERT: A  416 ASN cc_start: 0.9023 (m-40) cc_final: 0.8787 (t0)
REVERT: A  480 MET cc_start: 0.9565 (OUTLIER) cc_final: 0.9190 (mtp)
  outliers start: 5
  outliers final: 4
  residues processed: 37
  average time/residue: 1.8092
  time to fit residues: 70.5691
Evaluate side-chains
  37 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain A residue  480 MET
Chi-restraints excluded: chain A residue  572 ILE
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 76 optimal weight:    0.1980
   chunk 19 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 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 = 0.3257 r_free = 0.3257 target = 0.056822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.044097 restraints weight = 27197.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 4.07
r_work: 0.2758 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8877
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6705  Z= 0.120
  Angle     :  0.612  12.670   9128  Z= 0.292
  Chirality :  0.042   0.210    970
  Planarity :  0.003   0.038   1161
  Dihedral  :  5.625  52.754   1045
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.86 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 15.36 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.31), residues: 777
  helix:  2.00 (0.28), residues: 369
  sheet:  2.45 (0.82), residues: 45
  loop : -0.98 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 308 
 TYR   0.018   0.001   TYR B 369 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00742 (    5)
  link_NAG-ASN         : angle       3.79086 (   15)
  link_BETA1-4         : bond        0.00311 (    4)
  link_BETA1-4         : angle       1.81767 (   12)
  hydrogen bonds       : bond        0.04150 (  273)
  hydrogen bonds       : angle       3.60342 (  777)
  metal coordination   : bond        0.00052 (    2)
  SS BOND              : bond        0.00269 (    6)
  SS BOND              : angle       1.04537 (   12)
  covalent geometry    : bond        0.00283 ( 6688)
  covalent geometry    : angle       0.58926 ( 9089)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5704.17 seconds
wall clock time: 101 minutes 59.97 seconds (6119.97 seconds total)