Starting phenix.real_space_refine
on Mon Nov 17 16:27:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yf2_39208/11_2025/8yf2_39208.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yf2_39208/11_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yf2_39208/11_2025/8yf2_39208.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yf2_39208/11_2025/8yf2_39208.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yf2_39208/11_2025/8yf2_39208.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yf2_39208/11_2025/8yf2_39208.map"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 1.72, per 1000 atoms: 0.26
  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: 0.47
  Conformation dependent library (CDL) restraints added in 250.2 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: 0.16
  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: 0.93

  Time building geometry restraints manager: 0.61 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:             15.430
  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:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.640
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:6.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.010
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (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
 ARG   0.003   0.000   ARG A  95 
 TYR   0.014   0.001   TYR B 473 
 PHE   0.009   0.001   PHE A 438 
 TRP   0.014   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A 401 

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

*********************** 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  : 0.238 
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: 0.9436
  time to fit residues: 85.7357
Evaluate side-chains
  45 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 43
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.0386

-------------------------------------------------------------------------------
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
A 535 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.059130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.046449 restraints weight = 26404.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 4.03
r_work: 0.2818 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8824
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6705  Z= 0.153
  Angle     :  0.626   9.348   9128  Z= 0.317
  Chirality :  0.045   0.299    970
  Planarity :  0.004   0.037   1161
  Dihedral  :  7.594  55.348   1050
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.99 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  8.12 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.31), residues: 777
  helix:  1.18 (0.28), residues: 372
  sheet:  2.97 (0.75), residues: 44
  loop : -1.20 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 600 
 TYR   0.009   0.001   TYR A  50 
 PHE   0.008   0.001   PHE B 400 
 TRP   0.012   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6688)
  covalent geometry    : angle       0.60873 ( 9089)
  SS BOND              : bond        0.00297 (    6)
  SS BOND              : angle       0.98927 (   12)
  hydrogen bonds       : bond        0.05467 (  273)
  hydrogen bonds       : angle       4.11334 (  777)
  metal coordination   : bond        0.00071 (    2)
  link_BETA1-4         : bond        0.00395 (    4)
  link_BETA1-4         : angle       2.00118 (   12)
  link_NAG-ASN         : bond        0.00690 (    5)
  link_NAG-ASN         : angle       3.21286 (   15)

*********************** 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
  54 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8973 (mt-10)
REVERT: A  480 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.9113 (mtp)
  outliers start: 11
  outliers final: 1
  residues processed: 48
  average time/residue: 0.7104
  time to fit residues: 35.8136
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  : 0.269 
-------------------------------------------------------------------------------
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 14 optimal weight:   20.0000
   chunk 69 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0570
   chunk 71 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.1502

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3293 r_free = 0.3293 target = 0.057376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.044664 restraints weight = 26361.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 4.05
r_work: 0.2796 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6705  Z= 0.152
  Angle     :  0.589   8.261   9128  Z= 0.294
  Chirality :  0.044   0.275    970
  Planarity :  0.003   0.036   1161
  Dihedral  :  6.753  53.173   1045
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.35 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.29 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.31), residues: 777
  helix:  1.42 (0.28), residues: 376
  sheet:  2.92 (0.75), residues: 45
  loop : -1.27 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 466 
 TYR   0.009   0.001   TYR A  34 
 PHE   0.010   0.001   PHE B 338 
 TRP   0.010   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6688)
  covalent geometry    : angle       0.56946 ( 9089)
  SS BOND              : bond        0.00190 (    6)
  SS BOND              : angle       0.96283 (   12)
  hydrogen bonds       : bond        0.04980 (  273)
  hydrogen bonds       : angle       3.85442 (  777)
  metal coordination   : bond        0.00070 (    2)
  link_BETA1-4         : bond        0.00232 (    4)
  link_BETA1-4         : angle       1.89513 (   12)
  link_NAG-ASN         : bond        0.00809 (    5)
  link_NAG-ASN         : angle       3.31367 (   15)

*********************** 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
  45 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.337 
Fit side-chains
REVERT: B  465 GLU cc_start: 0.8933 (tt0) cc_final: 0.8228 (mt-10)
REVERT: B  516 GLU cc_start: 0.8619 (tt0) cc_final: 0.8226 (tm-30)
REVERT: A   30 GLU cc_start: 0.9237 (mm-30) cc_final: 0.9000 (mt-10)
REVERT: A  480 MET cc_start: 0.9603 (OUTLIER) cc_final: 0.9144 (mtp)
  outliers start: 6
  outliers final: 0
  residues processed: 42
  average time/residue: 0.8348
  time to fit residues: 36.5486
Evaluate side-chains
  35 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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 21 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 58 optimal weight:    0.1980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3273 r_free = 0.3273 target = 0.056691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.044065 restraints weight = 26490.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 4.00
r_work: 0.2776 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6705  Z= 0.166
  Angle     :  0.583   8.288   9128  Z= 0.291
  Chirality :  0.043   0.252    970
  Planarity :  0.003   0.036   1161
  Dihedral  :  6.422  53.144   1045
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.35 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.01 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.31), residues: 777
  helix:  1.62 (0.28), residues: 375
  sheet:  2.62 (0.75), residues: 45
  loop : -1.25 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 169 
 TYR   0.010   0.001   TYR A  34 
 PHE   0.009   0.001   PHE A 308 
 TRP   0.010   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 6688)
  covalent geometry    : angle       0.56274 ( 9089)
  SS BOND              : bond        0.00367 (    6)
  SS BOND              : angle       1.17447 (   12)
  hydrogen bonds       : bond        0.04896 (  273)
  hydrogen bonds       : angle       3.79794 (  777)
  metal coordination   : bond        0.00085 (    2)
  link_BETA1-4         : bond        0.00180 (    4)
  link_BETA1-4         : angle       1.85111 (   12)
  link_NAG-ASN         : bond        0.00735 (    5)
  link_NAG-ASN         : angle       3.34045 (   15)

*********************** 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
  47 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.268 
Fit side-chains
REVERT: B  465 GLU cc_start: 0.8859 (tt0) cc_final: 0.8590 (mt-10)
REVERT: B  516 GLU cc_start: 0.8615 (tt0) cc_final: 0.8230 (tm-30)
REVERT: A   30 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8974 (mt-10)
REVERT: A  480 MET cc_start: 0.9585 (OUTLIER) cc_final: 0.9198 (mtp)
  outliers start: 8
  outliers final: 1
  residues processed: 44
  average time/residue: 0.7511
  time to fit residues: 34.6400
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  : 0.274 
-------------------------------------------------------------------------------
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 15 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0970
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.058427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.045669 restraints weight = 26924.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 4.06
r_work: 0.2799 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8835
moved from start:          0.2580

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= 0.110
  Angle     :  0.561   9.109   9128  Z= 0.273
  Chirality :  0.042   0.242    970
  Planarity :  0.003   0.035   1161
  Dihedral  :  6.038  53.120   1045
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.22 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 12.03 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.31), residues: 777
  helix:  1.76 (0.28), residues: 374
  sheet:  2.51 (0.77), residues: 45
  loop : -1.15 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 403 
 TYR   0.020   0.001   TYR B 369 
 PHE   0.008   0.001   PHE A 315 
 TRP   0.009   0.001   TRP A 163 
 HIS   0.002   0.000   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6688)
  covalent geometry    : angle       0.54143 ( 9089)
  SS BOND              : bond        0.00341 (    6)
  SS BOND              : angle       0.93032 (   12)
  hydrogen bonds       : bond        0.04104 (  273)
  hydrogen bonds       : angle       3.63107 (  777)
  metal coordination   : bond        0.00068 (    2)
  link_BETA1-4         : bond        0.00334 (    4)
  link_BETA1-4         : angle       1.83777 (   12)
  link_NAG-ASN         : bond        0.00783 (    5)
  link_NAG-ASN         : angle       3.29096 (   15)

*********************** 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
  42 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.280 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8747 (mp0)
REVERT: B  516 GLU cc_start: 0.8599 (tt0) cc_final: 0.8229 (tm-30)
REVERT: A   30 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8964 (mt-10)
REVERT: A  480 MET cc_start: 0.9587 (mtm) cc_final: 0.9153 (mtp)
  outliers start: 5
  outliers final: 1
  residues processed: 40
  average time/residue: 0.6570
  time to fit residues: 27.7936
Evaluate side-chains
  33 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0670
   chunk 10 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 30 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.7920

-------------------------------------------------------------------------------
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 = 0.3288 r_free = 0.3288 target = 0.058154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.045505 restraints weight = 26762.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 4.06
r_work: 0.2792 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6705  Z= 0.117
  Angle     :  0.562   9.733   9128  Z= 0.274
  Chirality :  0.042   0.224    970
  Planarity :  0.003   0.032   1161
  Dihedral  :  5.806  52.978   1045
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.22 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 12.90 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.31), residues: 777
  helix:  1.85 (0.28), residues: 374
  sheet:  2.52 (0.77), residues: 45
  loop : -1.09 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.009   0.001   TYR A 516 
 PHE   0.007   0.001   PHE A 523 
 TRP   0.009   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6688)
  covalent geometry    : angle       0.54178 ( 9089)
  SS BOND              : bond        0.00241 (    6)
  SS BOND              : angle       0.98426 (   12)
  hydrogen bonds       : bond        0.04148 (  273)
  hydrogen bonds       : angle       3.60465 (  777)
  metal coordination   : bond        0.00078 (    2)
  link_BETA1-4         : bond        0.00283 (    4)
  link_BETA1-4         : angle       1.80082 (   12)
  link_NAG-ASN         : bond        0.00725 (    5)
  link_NAG-ASN         : angle       3.29295 (   15)

*********************** 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
  39 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.281 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8654 (mp0)
REVERT: A  480 MET cc_start: 0.9587 (OUTLIER) cc_final: 0.9226 (mtp)
  outliers start: 6
  outliers final: 2
  residues processed: 36
  average time/residue: 0.6290
  time to fit residues: 24.0104
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  : 0.258 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0570
   chunk 57 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   chunk 12 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.058475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.045930 restraints weight = 26457.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 4.00
r_work: 0.2808 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.2852

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= 0.105
  Angle     :  0.558   9.949   9128  Z= 0.269
  Chirality :  0.041   0.216    970
  Planarity :  0.003   0.036   1161
  Dihedral  :  5.582  53.121   1045
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.83 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 13.62 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.31), residues: 777
  helix:  1.91 (0.28), residues: 374
  sheet:  2.51 (0.78), residues: 45
  loop : -1.02 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.009   0.001   TYR A 516 
 PHE   0.006   0.001   PHE A 308 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6688)
  covalent geometry    : angle       0.53738 ( 9089)
  SS BOND              : bond        0.00163 (    6)
  SS BOND              : angle       0.90242 (   12)
  hydrogen bonds       : bond        0.03794 (  273)
  hydrogen bonds       : angle       3.53210 (  777)
  metal coordination   : bond        0.00102 (    2)
  link_BETA1-4         : bond        0.00302 (    4)
  link_BETA1-4         : angle       1.77490 (   12)
  link_NAG-ASN         : bond        0.00730 (    5)
  link_NAG-ASN         : angle       3.32621 (   15)

*********************** 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
  40 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.327 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8653 (mp0)
REVERT: A  455 MET cc_start: 0.9181 (tmm) cc_final: 0.8847 (tmm)
REVERT: A  480 MET cc_start: 0.9584 (OUTLIER) cc_final: 0.9155 (mtp)
  outliers start: 6
  outliers final: 4
  residues processed: 38
  average time/residue: 0.6303
  time to fit residues: 25.4493
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  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  362 VAL
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 40 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.055442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.042657 restraints weight = 27114.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 4.07
r_work: 0.2711 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8927
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.074   6705  Z= 0.282
  Angle     :  0.694  11.323   9128  Z= 0.344
  Chirality :  0.046   0.214    970
  Planarity :  0.004   0.040   1161
  Dihedral  :  5.905  52.401   1045
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.99 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 14.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.32), residues: 777
  helix:  1.91 (0.29), residues: 369
  sheet:  2.42 (0.76), residues: 45
  loop : -0.97 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.022   0.002   TYR B 369 
 PHE   0.012   0.001   PHE A 308 
 TRP   0.010   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00659 ( 6688)
  covalent geometry    : angle       0.67385 ( 9089)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       1.54633 (   12)
  hydrogen bonds       : bond        0.05823 (  273)
  hydrogen bonds       : angle       3.96340 (  777)
  metal coordination   : bond        0.00059 (    2)
  link_BETA1-4         : bond        0.00136 (    4)
  link_BETA1-4         : angle       1.78349 (   12)
  link_NAG-ASN         : bond        0.00653 (    5)
  link_NAG-ASN         : angle       3.72803 (   15)

*********************** 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
  39 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  480 MET cc_start: 0.9556 (OUTLIER) cc_final: 0.9224 (mtp)
  outliers start: 7
  outliers final: 5
  residues processed: 36
  average time/residue: 0.6560
  time to fit residues: 25.0377
Evaluate side-chains
  36 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain A residue   30 GLU
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 68 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0980
   chunk 59 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3268 r_free = 0.3268 target = 0.057276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.044667 restraints weight = 26848.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 4.04
r_work: 0.2769 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6705  Z= 0.123
  Angle     :  0.607  11.584   9128  Z= 0.294
  Chirality :  0.042   0.214    970
  Planarity :  0.003   0.042   1161
  Dihedral  :  5.628  53.210   1045
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.47 %
    Favored  : 96.40 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.32), residues: 777
  helix:  2.00 (0.29), residues: 369
  sheet:  2.31 (0.77), residues: 45
  loop : -0.93 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 169 
 TYR   0.011   0.001   TYR A 516 
 PHE   0.007   0.001   PHE A 308 
 TRP   0.009   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6688)
  covalent geometry    : angle       0.58655 ( 9089)
  SS BOND              : bond        0.00227 (    6)
  SS BOND              : angle       0.92617 (   12)
  hydrogen bonds       : bond        0.04277 (  273)
  hydrogen bonds       : angle       3.63502 (  777)
  metal coordination   : bond        0.00024 (    2)
  link_BETA1-4         : bond        0.00342 (    4)
  link_BETA1-4         : angle       1.77282 (   12)
  link_NAG-ASN         : bond        0.00714 (    5)
  link_NAG-ASN         : angle       3.52526 (   15)

*********************** 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: 5
    poor density    : 34
  time to evaluate  : 0.272 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8725 (mp0)
REVERT: B  516 GLU cc_start: 0.8659 (tt0) cc_final: 0.8442 (tm-30)
REVERT: A  249 MET cc_start: 0.9726 (mtp) cc_final: 0.9245 (mmm)
REVERT: A  455 MET cc_start: 0.9245 (tmm) cc_final: 0.8797 (tmm)
REVERT: A  480 MET cc_start: 0.9561 (OUTLIER) cc_final: 0.9149 (mtp)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.6383
  time to fit residues: 25.6632
Evaluate side-chains
  36 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  362 VAL
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 31 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0010
   chunk 29 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0770
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.3348

-------------------------------------------------------------------------------
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 = 0.3250 r_free = 0.3250 target = 0.056520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.043739 restraints weight = 26705.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 4.07
r_work: 0.2744 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8893
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6705  Z= 0.170
  Angle     :  0.629  12.353   9128  Z= 0.305
  Chirality :  0.043   0.201    970
  Planarity :  0.004   0.040   1161
  Dihedral  :  5.593  52.663   1045
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.73 %
    Favored  : 96.14 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.31), residues: 777
  helix:  2.00 (0.28), residues: 369
  sheet:  2.35 (0.77), residues: 45
  loop : -0.95 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.021   0.001   TYR B 369 
 PHE   0.009   0.001   PHE A 308 
 TRP   0.010   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 6688)
  covalent geometry    : angle       0.60912 ( 9089)
  SS BOND              : bond        0.00172 (    6)
  SS BOND              : angle       1.15369 (   12)
  hydrogen bonds       : bond        0.04682 (  273)
  hydrogen bonds       : angle       3.68173 (  777)
  metal coordination   : bond        0.00095 (    2)
  link_BETA1-4         : bond        0.00209 (    4)
  link_BETA1-4         : angle       1.74025 (   12)
  link_NAG-ASN         : bond        0.00635 (    5)
  link_NAG-ASN         : angle       3.52750 (   15)

********************** 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: 6
    poor density    : 32
  time to evaluate  : 0.330 
Fit side-chains
REVERT: B  406 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8725 (mp0)
REVERT: A  249 MET cc_start: 0.9729 (mtp) cc_final: 0.9242 (mmm)
REVERT: A  480 MET cc_start: 0.9553 (OUTLIER) cc_final: 0.9176 (mtp)
  outliers start: 6
  outliers final: 4
  residues processed: 36
  average time/residue: 0.6361
  time to fit residues: 24.2749
Evaluate side-chains
  34 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  362 VAL
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 18 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 = 0.3232 r_free = 0.3232 target = 0.055773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.043059 restraints weight = 27082.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 4.03
r_work: 0.2724 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8912
moved from start:          0.3165

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= 0.206
  Angle     :  0.661  13.226   9128  Z= 0.322
  Chirality :  0.044   0.204    970
  Planarity :  0.004   0.040   1161
  Dihedral  :  5.682  52.556   1045
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.73 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.31), residues: 777
  helix:  1.98 (0.28), residues: 369
  sheet:  2.44 (0.78), residues: 45
  loop : -1.00 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 177 
 TYR   0.013   0.001   TYR A  34 
 PHE   0.010   0.001   PHE A 308 
 TRP   0.010   0.001   TRP A 163 
 HIS   0.004   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 6688)
  covalent geometry    : angle       0.64104 ( 9089)
  SS BOND              : bond        0.00255 (    6)
  SS BOND              : angle       1.22342 (   12)
  hydrogen bonds       : bond        0.05130 (  273)
  hydrogen bonds       : angle       3.79863 (  777)
  metal coordination   : bond        0.00126 (    2)
  link_BETA1-4         : bond        0.00196 (    4)
  link_BETA1-4         : angle       1.73729 (   12)
  link_NAG-ASN         : bond        0.00633 (    5)
  link_NAG-ASN         : angle       3.61295 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2445.27 seconds
wall clock time: 42 minutes 35.77 seconds (2555.77 seconds total)