Starting phenix.real_space_refine
on Sat May 10 15:01:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yf2_39208/05_2025/8yf2_39208.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yf2_39208/05_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_39208/05_2025/8yf2_39208.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yf2_39208/05_2025/8yf2_39208.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yf2_39208/05_2025/8yf2_39208.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yf2_39208/05_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-5687/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: 6.86, per 1000 atoms: 1.05
  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: 1.61
  Conformation dependent library (CDL) restraints added in 840.2 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: 0.57
  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: 1.55

  Time building geometry restraints manager: 1.90 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:             10.670
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.340
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.010
-------------------------------------------------------------------------------
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  : 0.744 
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: 1.8450
  time to fit residues: 168.0581
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  : 0.737 
-------------------------------------------------------------------------------
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 = 0.047012 restraints weight = 25889.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 3.99
r_work: 0.2834 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
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  : 0.690 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8986 (mt-10)
REVERT: A  480 MET cc_start: 0.9621 (OUTLIER) cc_final: 0.9197 (mtp)
  outliers start: 12
  outliers final: 1
  residues processed: 48
  average time/residue: 1.4163
  time to fit residues: 71.6302
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  : 0.754 
-------------------------------------------------------------------------------
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:    0.0000
   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:    0.4980
   chunk 76 optimal weight:    6.9990
   overall best weight:    1.4188

-------------------------------------------------------------------------------
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 = 0.3284 r_free = 0.3284 target = 0.058000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.045192 restraints weight = 26634.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 4.09
r_work: 0.2783 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6705  Z= 0.179
  Angle     :  0.605   8.147   9128  Z= 0.303
  Chirality :  0.044   0.274    970
  Planarity :  0.003   0.036   1161
  Dihedral  :  6.795  53.068   1045
  Min Nonbonded Distance : 2.559

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:  0.49 (0.31), residues: 777
  helix:  1.39 (0.28), residues: 378
  sheet:  2.90 (0.75), residues: 45
  loop : -1.26 (0.32), residues: 354

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   0.010   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        0.00770 (    5)
  link_NAG-ASN         : angle       3.37186 (   15)
  link_BETA1-4         : bond        0.00280 (    4)
  link_BETA1-4         : angle       1.87563 (   12)
  hydrogen bonds       : bond        0.05215 (  273)
  hydrogen bonds       : angle       3.89216 (  777)
  metal coordination   : bond        0.00049 (    2)
  SS BOND              : bond        0.00223 (    6)
  SS BOND              : angle       1.03493 (   12)
  covalent geometry    : bond        0.00416 ( 6688)
  covalent geometry    : angle       0.58504 ( 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  : 0.729 
Fit side-chains
REVERT: B  516 GLU cc_start: 0.8614 (tt0) cc_final: 0.8213 (tm-30)
REVERT: A   30 GLU cc_start: 0.9243 (mm-30) cc_final: 0.9022 (mt-10)
REVERT: A  480 MET cc_start: 0.9607 (OUTLIER) cc_final: 0.9148 (mtp)
  outliers start: 6
  outliers final: 0
  residues processed: 43
  average time/residue: 1.6231
  time to fit residues: 73.2335
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  : 0.748 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3252 r_free = 0.3252 target = 0.056688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.044008 restraints weight = 26817.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 4.03
r_work: 0.2749 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8893
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   6705  Z= 0.208
  Angle     :  0.618   8.393   9128  Z= 0.310
  Chirality :  0.044   0.253    970
  Planarity :  0.004   0.037   1161
  Dihedral  :  6.511  53.016   1045
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.60 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 11.16 %
    Favored  : 87.97 %
  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:  0.61 (0.31), residues: 777
  helix:  1.62 (0.28), residues: 375
  sheet:  2.59 (0.74), residues: 45
  loop : -1.28 (0.32), residues: 357

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   0.010   0.001   PHE A 308 
 TYR   0.012   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       3.44528 (   15)
  link_BETA1-4         : bond        0.00201 (    4)
  link_BETA1-4         : angle       1.87149 (   12)
  hydrogen bonds       : bond        0.05360 (  273)
  hydrogen bonds       : angle       3.92489 (  777)
  metal coordination   : bond        0.00120 (    2)
  SS BOND              : bond        0.00213 (    6)
  SS BOND              : angle       1.14639 (   12)
  covalent geometry    : bond        0.00487 ( 6688)
  covalent geometry    : angle       0.59814 ( 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  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: B  465 GLU cc_start: 0.8827 (tt0) cc_final: 0.8512 (mt-10)
REVERT: B  516 GLU cc_start: 0.8624 (tt0) cc_final: 0.8342 (tm-30)
REVERT: A   30 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9019 (mt-10)
REVERT: A  480 MET cc_start: 0.9581 (OUTLIER) cc_final: 0.9185 (mtp)
  outliers start: 6
  outliers final: 2
  residues processed: 43
  average time/residue: 1.5825
  time to fit residues: 71.4826
Evaluate side-chains
  37 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  378 LYS
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:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 58 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    2.0588

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.055461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.042625 restraints weight = 27116.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 4.07
r_work: 0.2719 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8914
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071   6705  Z= 0.242
  Angle     :  0.647   9.034   9128  Z= 0.324
  Chirality :  0.045   0.251    970
  Planarity :  0.004   0.039   1161
  Dihedral  :  6.380  52.360   1045
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.60 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 13.04 %
    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:  0.65 (0.31), residues: 777
  helix:  1.71 (0.28), residues: 374
  sheet:  2.47 (0.76), residues: 45
  loop : -1.31 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.009   0.001   PHE B 338 
 TYR   0.020   0.002   TYR B 369 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00771 (    5)
  link_NAG-ASN         : angle       3.64517 (   15)
  link_BETA1-4         : bond        0.00153 (    4)
  link_BETA1-4         : angle       1.83889 (   12)
  hydrogen bonds       : bond        0.05659 (  273)
  hydrogen bonds       : angle       4.02204 (  777)
  metal coordination   : bond        0.00147 (    2)
  SS BOND              : bond        0.00410 (    6)
  SS BOND              : angle       1.54343 (   12)
  covalent geometry    : bond        0.00568 ( 6688)
  covalent geometry    : angle       0.62533 ( 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
  44 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8648 (mp0)
REVERT: B  465 GLU cc_start: 0.8832 (tt0) cc_final: 0.8577 (mt-10)
REVERT: A   30 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8870 (mm-30)
REVERT: A  416 ASN cc_start: 0.9053 (m-40) cc_final: 0.8831 (t0)
REVERT: A  480 MET cc_start: 0.9566 (OUTLIER) cc_final: 0.9173 (mtp)
  outliers start: 8
  outliers final: 1
  residues processed: 41
  average time/residue: 1.2690
  time to fit residues: 55.2488
Evaluate side-chains
  36 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain A residue  480 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 57 optimal weight:    0.0870
   chunk 2 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.3266 r_free = 0.3266 target = 0.057248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.044594 restraints weight = 26457.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 4.04
r_work: 0.2768 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6705  Z= 0.109
  Angle     :  0.587  10.416   9128  Z= 0.283
  Chirality :  0.042   0.234    970
  Planarity :  0.003   0.036   1161
  Dihedral  :  6.006  53.151   1045
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.96 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 13.91 %
    Favored  : 85.65 %
  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:  0.85 (0.31), residues: 777
  helix:  1.86 (0.28), residues: 375
  sheet:  2.38 (0.77), residues: 45
  loop : -1.16 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 566 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.007   0.001   PHE B 392 
 TYR   0.012   0.001   TYR A 516 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00792 (    5)
  link_NAG-ASN         : angle       3.44447 (   15)
  link_BETA1-4         : bond        0.00346 (    4)
  link_BETA1-4         : angle       1.87055 (   12)
  hydrogen bonds       : bond        0.04322 (  273)
  hydrogen bonds       : angle       3.69896 (  777)
  metal coordination   : bond        0.00192 (    2)
  SS BOND              : bond        0.00197 (    6)
  SS BOND              : angle       0.90097 (   12)
  covalent geometry    : bond        0.00246 ( 6688)
  covalent geometry    : angle       0.56611 ( 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
  38 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8653 (mp0)
REVERT: B  465 GLU cc_start: 0.8746 (tt0) cc_final: 0.8536 (mt-10)
REVERT: B  516 GLU cc_start: 0.8583 (tt0) cc_final: 0.8338 (tm-30)
REVERT: A  416 ASN cc_start: 0.9020 (m-40) cc_final: 0.8812 (t0)
REVERT: A  480 MET cc_start: 0.9567 (mtm) cc_final: 0.9206 (mtp)
  outliers start: 3
  outliers final: 2
  residues processed: 38
  average time/residue: 1.3612
  time to fit residues: 54.8084
Evaluate side-chains
  36 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 42 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 = 0.3242 r_free = 0.3242 target = 0.056182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.043498 restraints weight = 26622.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 4.02
r_work: 0.2740 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
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      :  0.004   0.051   6705  Z= 0.177
  Angle     :  0.609  10.598   9128  Z= 0.297
  Chirality :  0.043   0.221    970
  Planarity :  0.004   0.036   1161
  Dihedral  :  5.937  52.538   1045
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.22 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.35 %
    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:  0.93 (0.31), residues: 777
  helix:  1.91 (0.28), residues: 375
  sheet:  2.46 (0.77), residues: 45
  loop : -1.10 (0.32), residues: 357

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   0.021   0.001   TYR B 369 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00708 (    5)
  link_NAG-ASN         : angle       3.58241 (   15)
  link_BETA1-4         : bond        0.00164 (    4)
  link_BETA1-4         : angle       1.81489 (   12)
  hydrogen bonds       : bond        0.04925 (  273)
  hydrogen bonds       : angle       3.79811 (  777)
  metal coordination   : bond        0.00151 (    2)
  SS BOND              : bond        0.00246 (    6)
  SS BOND              : angle       1.22271 (   12)
  covalent geometry    : bond        0.00418 ( 6688)
  covalent geometry    : angle       0.58682 ( 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
  41 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.692 
Fit side-chains
REVERT: B  465 GLU cc_start: 0.8800 (tt0) cc_final: 0.8547 (mt-10)
REVERT: B  516 GLU cc_start: 0.8598 (tt0) cc_final: 0.8350 (tm-30)
REVERT: A  416 ASN cc_start: 0.9037 (m-40) cc_final: 0.8824 (t0)
REVERT: A  480 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9186 (mtp)
  outliers start: 6
  outliers final: 2
  residues processed: 37
  average time/residue: 1.3944
  time to fit residues: 54.5527
Evaluate side-chains
  36 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   chunk 8 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3262 r_free = 0.3262 target = 0.057089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.044426 restraints weight = 26677.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 4.01
r_work: 0.2765 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.3034

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= 0.126
  Angle     :  0.587  11.308   9128  Z= 0.284
  Chirality :  0.042   0.217    970
  Planarity :  0.003   0.040   1161
  Dihedral  :  5.730  52.988   1045
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.70 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.20 %
    Favored  : 84.93 %
  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:  1.04 (0.31), residues: 777
  helix:  2.00 (0.28), residues: 369
  sheet:  2.39 (0.78), residues: 45
  loop : -0.97 (0.33), 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   0.007   0.001   PHE B 338 
 TYR   0.010   0.001   TYR A 516 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00751 (    5)
  link_NAG-ASN         : angle       3.52927 (   15)
  link_BETA1-4         : bond        0.00301 (    4)
  link_BETA1-4         : angle       1.81741 (   12)
  hydrogen bonds       : bond        0.04227 (  273)
  hydrogen bonds       : angle       3.64373 (  777)
  metal coordination   : bond        0.00127 (    2)
  SS BOND              : bond        0.00187 (    6)
  SS BOND              : angle       0.96006 (   12)
  covalent geometry    : bond        0.00300 ( 6688)
  covalent geometry    : angle       0.56609 ( 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
  42 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.733 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8747 (mp0)
REVERT: B  465 GLU cc_start: 0.8752 (tt0) cc_final: 0.8499 (mt-10)
REVERT: B  516 GLU cc_start: 0.8611 (tt0) cc_final: 0.8405 (tm-30)
REVERT: A  416 ASN cc_start: 0.9017 (m-40) cc_final: 0.8802 (t0)
REVERT: A  480 MET cc_start: 0.9562 (OUTLIER) cc_final: 0.9185 (mtp)
  outliers start: 6
  outliers final: 2
  residues processed: 40
  average time/residue: 1.3100
  time to fit residues: 55.5114
Evaluate side-chains
  36 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0670
   chunk 42 optimal weight:    0.2980
   chunk 54 optimal weight:    3.9990
   chunk 14 optimal weight:    0.1980
   chunk 66 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.4118

-------------------------------------------------------------------------------
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 = 0.3292 r_free = 0.3292 target = 0.058389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.045701 restraints weight = 27223.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 4.08
r_work: 0.2802 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6705  Z= 0.099
  Angle     :  0.578  11.668   9128  Z= 0.276
  Chirality :  0.041   0.203    970
  Planarity :  0.003   0.040   1161
  Dihedral  :  5.429  53.084   1045
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.09 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 14.78 %
    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:  1.17 (0.32), residues: 777
  helix:  2.20 (0.28), residues: 360
  sheet:  2.09 (0.79), residues: 47
  loop : -0.90 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 566 
 HIS   0.001   0.000   HIS A 378 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.021   0.001   TYR B 369 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00743 (    5)
  link_NAG-ASN         : angle       3.51845 (   15)
  link_BETA1-4         : bond        0.00379 (    4)
  link_BETA1-4         : angle       1.77533 (   12)
  hydrogen bonds       : bond        0.03530 (  273)
  hydrogen bonds       : angle       3.50245 (  777)
  metal coordination   : bond        0.00095 (    2)
  SS BOND              : bond        0.00175 (    6)
  SS BOND              : angle       0.83249 (   12)
  covalent geometry    : bond        0.00227 ( 6688)
  covalent geometry    : angle       0.55674 ( 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
  39 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.712 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8770 (mp0)
REVERT: B  465 GLU cc_start: 0.8709 (tt0) cc_final: 0.8495 (mt-10)
REVERT: B  516 GLU cc_start: 0.8612 (tt0) cc_final: 0.8389 (tm-30)
REVERT: A  480 MET cc_start: 0.9559 (OUTLIER) cc_final: 0.9209 (mtp)
  outliers start: 4
  outliers final: 2
  residues processed: 37
  average time/residue: 1.2925
  time to fit residues: 50.8242
Evaluate side-chains
  35 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
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
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 24 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 51 optimal weight:    0.0060
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.1602

-------------------------------------------------------------------------------
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 = 0.3260 r_free = 0.3260 target = 0.057086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.044431 restraints weight = 27155.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 4.06
r_work: 0.2762 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6705  Z= 0.149
  Angle     :  0.614  13.985   9128  Z= 0.294
  Chirality :  0.042   0.199    970
  Planarity :  0.003   0.039   1161
  Dihedral  :  5.430  52.854   1045
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.96 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 15.07 %
    Favored  : 84.35 %
  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:  1.15 (0.32), residues: 777
  helix:  2.07 (0.28), residues: 369
  sheet:  2.48 (0.79), residues: 45
  loop : -0.90 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.007   0.001   PHE A 523 
 TYR   0.010   0.001   TYR A  34 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00666 (    5)
  link_NAG-ASN         : angle       3.59612 (   15)
  link_BETA1-4         : bond        0.00236 (    4)
  link_BETA1-4         : angle       1.74060 (   12)
  hydrogen bonds       : bond        0.04271 (  273)
  hydrogen bonds       : angle       3.58947 (  777)
  metal coordination   : bond        0.00163 (    2)
  SS BOND              : bond        0.00188 (    6)
  SS BOND              : angle       1.05356 (   12)
  covalent geometry    : bond        0.00352 ( 6688)
  covalent geometry    : angle       0.59349 ( 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
  36 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.744 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8738 (mp0)
REVERT: A  480 MET cc_start: 0.9559 (OUTLIER) cc_final: 0.9221 (mtp)
  outliers start: 4
  outliers final: 2
  residues processed: 35
  average time/residue: 1.4103
  time to fit residues: 52.3313
Evaluate side-chains
  32 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0070
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.1604

-------------------------------------------------------------------------------
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 = 0.3255 r_free = 0.3255 target = 0.056873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.044174 restraints weight = 27393.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 4.08
r_work: 0.2755 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8881
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6705  Z= 0.149
  Angle     :  0.620  13.485   9128  Z= 0.297
  Chirality :  0.042   0.201    970
  Planarity :  0.003   0.040   1161
  Dihedral  :  5.461  52.913   1045
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.47 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.64 %
    Favored  : 84.49 %
  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:  1.14 (0.32), residues: 777
  helix:  2.05 (0.28), residues: 369
  sheet:  2.53 (0.81), residues: 45
  loop : -0.90 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.007   0.001   PHE A 308 
 TYR   0.021   0.001   TYR B 369 
 ARG   0.002   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00658 (    5)
  link_NAG-ASN         : angle       3.56732 (   15)
  link_BETA1-4         : bond        0.00248 (    4)
  link_BETA1-4         : angle       1.71028 (   12)
  hydrogen bonds       : bond        0.04343 (  273)
  hydrogen bonds       : angle       3.61156 (  777)
  metal coordination   : bond        0.00121 (    2)
  SS BOND              : bond        0.00123 (    6)
  SS BOND              : angle       1.13298 (   12)
  covalent geometry    : bond        0.00354 ( 6688)
  covalent geometry    : angle       0.59957 ( 9089)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4881.68 seconds
wall clock time: 85 minutes 59.39 seconds (5159.39 seconds total)