Starting phenix.real_space_refine
on Fri Aug 22 17:45:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i9h_35272/08_2025/8i9h_35272.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i9h_35272/08_2025/8i9h_35272.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i9h_35272/08_2025/8i9h_35272.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i9h_35272/08_2025/8i9h_35272.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i9h_35272/08_2025/8i9h_35272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i9h_35272/08_2025/8i9h_35272.map"
  }
  resolution = 3.6
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4161      2.51       5
     N    1063      2.21       5
     O    1253      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6514
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
    Chain: "E"
      Number of atoms: 1462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1462
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 11, 'TRANS': 171}
          Chain breaks: 1
    Chain: "B"
      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: "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: "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: "G"
      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: "H"
      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: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.43, per 1000 atoms: 0.22
  Number of scatterers: 6514
  At special positions: 0
  Unit cell: (105.439, 86.96, 109.787, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1253      8.00
     N    1063      7.00
     C    4161      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    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
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 322 "
      " NAG B   1 " - " ASN A  53 "
      " NAG C   1 " - " ASN A  90 "
      " NAG D   1 " - " ASN A 103 "
      " NAG F   1 " - " ASN A 432 "
      " NAG G   1 " - " ASN A 546 "
      " NAG H   1 " - " ASN E 343 "
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 246.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1472

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      50.1% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 31
      removed outlier: 3.885A  pdb=" N   LYS A  26 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   PHE A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LYS A  31 " --> pdb=" O   THR A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 52
      removed outlier: 4.038A  pdb=" N   TYR A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TYR A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
      removed outlier: 3.854A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA A  65 " --> pdb=" O   ASN A  61 " (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 102
      removed outlier: 3.829A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.558A  pdb=" N   SER A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 155
      removed outlier: 3.789A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 171
      removed outlier: 3.800A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 193
      removed outlier: 4.571A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.552A  pdb=" N   TYR A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 230
      removed outlier: 4.317A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 249
      removed outlier: 4.422A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 305 through 319
      removed outlier: 3.778A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY A 319 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 4.025A  pdb=" N   ASN A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 4.040A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.554A  pdb=" N   LEU A 392 " --> pdb=" O   PRO A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 3.801A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
      removed outlier: 3.690A  pdb=" N   SER A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   GLY A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 444
      removed outlier: 3.603A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 472 through 484
    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: 4.099A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN A 531 " --> pdb=" O   GLU A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.526A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.709A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ARG A 559 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 570
    Processing helix  chain 'A' and resid 581 through 596
      removed outlier: 3.558A  pdb=" N   LEU A 585 " --> pdb=" O   VAL A 581 " (cutoff:3.500A)
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'E' and resid 337 through 341
      removed outlier: 3.702A  pdb=" N   GLU E 340 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 349 through 353
    Processing helix  chain 'E' and resid 364 through 368
      removed outlier: 4.094A  pdb=" N   VAL E 367 " --> pdb=" O   ASP E 364 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 390
    Processing helix  chain 'E' and resid 403 through 410
      removed outlier: 3.842A  pdb=" N   GLU E 406 " --> pdb=" O   ARG E 403 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   SER E 408 " --> pdb=" O   ASN E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 438 through 443
      removed outlier: 3.570A  pdb=" N   ASP E 442 " --> pdb=" O   SER E 438 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER E 443 " --> pdb=" O   ASN E 439 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 438 through 443'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.323A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352
      removed outlier: 3.704A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358
      removed outlier: 4.461A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE E 434 " --> pdb=" O   VAL E 511 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454
      removed outlier: 3.684A  pdb=" N   GLN E 493 " --> pdb=" O   TYR E 453 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474

    243 hydrogen bonds defined for protein.
    666 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: 0.75

  Time building geometry restraints manager: 0.48 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: 2061
        1.34 -     1.46: 1712
        1.46 -     1.58: 2864
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6695
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.462 -0.056 2.00e-02 2.50e+03 7.95e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 3.96e+00
  bond pdb=" CA  ASN A 149 "
       pdb=" C   ASN A 149 "
    ideal  model  delta    sigma   weight residual
    1.523  1.496  0.027 1.41e-02 5.03e+03 3.54e+00
  bond pdb=" C1  NAG H   2 "
       pdb=" O5  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.43e+00
  bond pdb=" CA  HIS E 339 "
       pdb=" C   HIS E 339 "
    ideal  model  delta    sigma   weight residual
    1.522  1.496  0.025 1.72e-02 3.38e+03 2.18e+00
  ... (remaining 6690 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 8525
        1.32 -     2.64: 474
        2.64 -     3.96: 71
        3.96 -     5.28: 22
        5.28 -     6.60: 5
  Bond angle restraints: 9097
  Sorted by residual:
  angle pdb=" N   ILE A  21 "
        pdb=" CA  ILE A  21 "
        pdb=" C   ILE A  21 "
      ideal   model   delta    sigma   weight residual
     112.29  107.52    4.77 9.40e-01 1.13e+00 2.57e+01
  angle pdb=" N   GLU A 197 "
        pdb=" CA  GLU A 197 "
        pdb=" CB  GLU A 197 "
      ideal   model   delta    sigma   weight residual
     114.17  109.20    4.97 1.14e+00 7.69e-01 1.90e+01
  angle pdb=" CA  PRO A 138 "
        pdb=" C   PRO A 138 "
        pdb=" N   GLN A 139 "
      ideal   model   delta    sigma   weight residual
     116.45  119.77   -3.32 8.50e-01 1.38e+00 1.52e+01
  angle pdb=" CA  PRO A 138 "
        pdb=" C   PRO A 138 "
        pdb=" O   PRO A 138 "
      ideal   model   delta    sigma   weight residual
     121.38  118.61    2.77 7.70e-01 1.69e+00 1.30e+01
  angle pdb=" N   ASP A 509 "
        pdb=" CA  ASP A 509 "
        pdb=" C   ASP A 509 "
      ideal   model   delta    sigma   weight residual
     111.52  116.55   -5.03 1.40e+00 5.10e-01 1.29e+01
  ... (remaining 9092 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3526
       17.99 -    35.98: 434
       35.98 -    53.97: 130
       53.97 -    71.95: 19
       71.95 -    89.94: 7
  Dihedral angle restraints: 4116
    sinusoidal: 1824
      harmonic: 2292
  Sorted by residual:
  dihedral pdb=" CA  CYS A 344 "
           pdb=" C   CYS A 344 "
           pdb=" N   HIS A 345 "
           pdb=" CA  HIS A 345 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.30   19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   60.27   32.73     1      1.00e+01 1.00e-02 1.52e+01
  dihedral pdb=" CA  GLY A 337 "
           pdb=" C   GLY A 337 "
           pdb=" N   ASN A 338 "
           pdb=" CA  ASN A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.64  -19.36     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 4113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 889
       0.079 -    0.158: 92
       0.158 -    0.237: 3
       0.237 -    0.316: 1
       0.316 -    0.395: 1
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A  90 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.89e+00
  chirality pdb=" C4  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" C5  NAG D   1 "
            pdb=" O4  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.25   -0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C2  NAG D   2 "
            pdb=" C1  NAG D   2 "
            pdb=" C3  NAG D   2 "
            pdb=" N2  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.30   -0.20 2.00e-01 2.50e+01 9.66e-01
  ... (remaining 983 not shown)

  Planarity restraints: 1168
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 372 "   -0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO E 373 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO E 373 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E 373 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 462 "   -0.028 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO E 463 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO E 463 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E 463 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "   -0.026 5.00e-02 4.00e+02   3.86e-02 2.39e+00
        pdb=" N   PRO A 583 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1165 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 184
        2.69 -     3.24: 6348
        3.24 -     3.79: 9469
        3.79 -     4.35: 11957
        4.35 -     4.90: 20385
  Nonbonded interactions: 48343
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 111 "
            pdb=" OD1 ASP A 111 "
     model   vdw
     2.135 3.120
  nonbonded pdb=" O   ASN E 439 "
            pdb=" OG  SER E 443 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER E 349 "
            pdb=" O   LEU E 452 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OD1 ASP A 382 "
            pdb=" OH  TYR A 385 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" NH2 ARG E 357 "
            pdb=" O   ILE E 358 "
     model   vdw
     2.277 3.120
  ... (remaining 48338 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 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.740
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.370
  Find NCS groups from input model:        0.030
  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:0.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   6714  Z= 0.286
  Angle     :  0.741  10.767   9148  Z= 0.399
  Chirality :  0.050   0.395    986
  Planarity :  0.004   0.044   1161
  Dihedral  : 16.884  89.943   2626
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 19.24 %
    Favored  : 73.18 %
  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 aren not related in a simple way.
  whole: -4.33 (0.24), residues: 774
  helix: -2.10 (0.23), residues: 359
  sheet: -2.11 (0.64), residues: 48
  loop : -3.87 (0.24), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 169 
 TYR   0.017   0.001   TYR A 183 
 PHE   0.012   0.002   PHE E 400 
 TRP   0.010   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 ( 6695)
  covalent geometry    : angle       0.70773 ( 9097)
  SS BOND              : bond        0.00276 (    6)
  SS BOND              : angle       3.43378 (   12)
  hydrogen bonds       : bond        0.16826 (  243)
  hydrogen bonds       : angle       6.39674 (  666)
  link_BETA1-4         : bond        0.00634 (    6)
  link_BETA1-4         : angle       3.18792 (   18)
  link_NAG-ASN         : bond        0.00643 (    7)
  link_NAG-ASN         : angle       2.56795 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 87
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8873 (tmtt) cc_final: 0.8352 (tptp)
REVERT: A  115 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7492 (tpt170)
REVERT: A  154 ASN cc_start: 0.8106 (m-40) cc_final: 0.7866 (t0)
REVERT: A  156 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8576 (tt)
REVERT: A  224 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6804 (mp0)
REVERT: A  367 ASP cc_start: 0.6928 (p0) cc_final: 0.6700 (p0)
REVERT: E  414 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9015 (tp40)
REVERT: E  466 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7425 (ptm160)
  outliers start: 52
  outliers final: 41
  residues processed: 134
  average time/residue: 0.0696
  time to fit residues: 12.5070
Evaluate side-chains
  120 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 76
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  432 ASN
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  388 ASN
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  418 ILE
Chi-restraints excluded: chain E residue  425 LEU
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  494 SER
Chi-restraints excluded: chain E residue  500 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 102 GLN
A 239 HIS
A 305 GLN
A 340 GLN
A 374 HIS
A 378 HIS
A 437 ASN
A 472 GLN
A 505 HIS
A 522 GLN
A 535 HIS
A 599 ASN
** E 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 450 ASN
E 487 ASN
** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.103905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.085799 restraints weight = 11438.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.089115 restraints weight = 5546.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.091394 restraints weight = 3377.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.092962 restraints weight = 2359.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.094024 restraints weight = 1810.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6714  Z= 0.119
  Angle     :  0.646  14.854   9148  Z= 0.305
  Chirality :  0.045   0.307    986
  Planarity :  0.004   0.058   1161
  Dihedral  :  9.491  58.768   1192
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 22.01 %
    Favored  : 72.89 %
  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 aren not related in a simple way.
  whole: -3.05 (0.27), residues: 774
  helix: -0.95 (0.27), residues: 363
  sheet: -1.53 (0.67), residues: 49
  loop : -3.33 (0.26), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 115 
 TYR   0.011   0.001   TYR A 183 
 PHE   0.013   0.001   PHE A 428 
 TRP   0.009   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6695)
  covalent geometry    : angle       0.62004 ( 9097)
  SS BOND              : bond        0.00595 (    6)
  SS BOND              : angle       1.48942 (   12)
  hydrogen bonds       : bond        0.04342 (  243)
  hydrogen bonds       : angle       4.17834 (  666)
  link_BETA1-4         : bond        0.00478 (    6)
  link_BETA1-4         : angle       2.36857 (   18)
  link_NAG-ASN         : bond        0.00613 (    7)
  link_NAG-ASN         : angle       3.01277 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 81
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8432 (tptp)
REVERT: A   82 MET cc_start: 0.7797 (ttp) cc_final: 0.6860 (tmm)
REVERT: A  201 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8212 (t70)
REVERT: A  340 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7307 (mm110)
REVERT: A  363 LYS cc_start: 0.8247 (pttp) cc_final: 0.7877 (pttm)
REVERT: A  474 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8469 (mmm)
REVERT: E  414 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9013 (tp40)
REVERT: E  466 ARG cc_start: 0.8350 (ptm160) cc_final: 0.8080 (ptm160)
  outliers start: 35
  outliers final: 20
  residues processed: 108
  average time/residue: 0.0577
  time to fit residues: 8.8639
Evaluate side-chains
  99 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  467 ASP
Chi-restraints excluded: chain E residue  468 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 340 GLN
** E 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 487 ASN
** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.101618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.083622 restraints weight = 11448.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.086829 restraints weight = 5641.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.089020 restraints weight = 3477.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.090496 restraints weight = 2456.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.091559 restraints weight = 1908.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6714  Z= 0.209
  Angle     :  0.655  11.731   9148  Z= 0.313
  Chirality :  0.047   0.297    986
  Planarity :  0.004   0.058   1161
  Dihedral  :  8.132  59.890   1143
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 23.47 %
    Favored  : 71.72 %
  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 aren not related in a simple way.
  whole: -2.64 (0.28), residues: 774
  helix: -0.55 (0.28), residues: 363
  sheet: -1.28 (0.69), residues: 48
  loop : -3.19 (0.27), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 457 
 TYR   0.014   0.001   TYR A 183 
 PHE   0.012   0.001   PHE A 327 
 TRP   0.010   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 6695)
  covalent geometry    : angle       0.63028 ( 9097)
  SS BOND              : bond        0.00386 (    6)
  SS BOND              : angle       2.07491 (   12)
  hydrogen bonds       : bond        0.04683 (  243)
  hydrogen bonds       : angle       4.16287 (  666)
  link_BETA1-4         : bond        0.00485 (    6)
  link_BETA1-4         : angle       2.46108 (   18)
  link_NAG-ASN         : bond        0.00410 (    7)
  link_NAG-ASN         : angle       2.69055 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 80
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8961 (tmtt) cc_final: 0.8395 (tptp)
REVERT: A   82 MET cc_start: 0.7780 (ttp) cc_final: 0.6737 (tmm)
REVERT: A  201 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8215 (t0)
REVERT: A  323 MET cc_start: 0.8161 (mmm) cc_final: 0.7850 (mmm)
REVERT: A  340 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7649 (mm110)
REVERT: A  479 GLU cc_start: 0.8504 (tp30) cc_final: 0.8251 (tp30)
REVERT: E  414 GLN cc_start: 0.9271 (mm-40) cc_final: 0.9012 (tp40)
  outliers start: 33
  outliers final: 23
  residues processed: 107
  average time/residue: 0.0564
  time to fit residues: 8.6225
Evaluate side-chains
  100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  340 GLN
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  467 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0770
   chunk 40 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
E 339 HIS
E 487 ASN
E 493 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.105131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.086612 restraints weight = 11540.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.089870 restraints weight = 5715.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.092121 restraints weight = 3550.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.093681 restraints weight = 2523.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.094730 restraints weight = 1964.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6714  Z= 0.115
  Angle     :  0.632  21.293   9148  Z= 0.290
  Chirality :  0.045   0.299    986
  Planarity :  0.004   0.057   1161
  Dihedral  :  7.738  59.636   1141
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 24.05 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.19 (0.29), residues: 774
  helix: -0.15 (0.29), residues: 359
  sheet: -1.21 (0.71), residues: 49
  loop : -2.93 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 219 
 TYR   0.011   0.001   TYR A 183 
 PHE   0.011   0.001   PHE A 428 
 TRP   0.008   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6695)
  covalent geometry    : angle       0.60565 ( 9097)
  SS BOND              : bond        0.00629 (    6)
  SS BOND              : angle       2.35356 (   12)
  hydrogen bonds       : bond        0.03866 (  243)
  hydrogen bonds       : angle       3.87977 (  666)
  link_BETA1-4         : bond        0.00458 (    6)
  link_BETA1-4         : angle       2.35528 (   18)
  link_NAG-ASN         : bond        0.00580 (    7)
  link_NAG-ASN         : angle       2.69974 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 79
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8934 (tmtt) cc_final: 0.8634 (tppt)
REVERT: A   82 MET cc_start: 0.7592 (ttp) cc_final: 0.6526 (tmm)
REVERT: A  201 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.7981 (t0)
REVERT: A  249 MET cc_start: 0.8145 (ttp) cc_final: 0.7889 (tmm)
REVERT: A  256 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8851 (mm)
REVERT: A  306 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7459 (tpp-160)
REVERT: A  479 GLU cc_start: 0.8432 (tp30) cc_final: 0.8204 (tp30)
REVERT: E  414 GLN cc_start: 0.9250 (mm-40) cc_final: 0.8981 (tp40)
REVERT: E  466 ARG cc_start: 0.8385 (ptm160) cc_final: 0.8113 (ptm160)
  outliers start: 31
  outliers final: 19
  residues processed: 104
  average time/residue: 0.0594
  time to fit residues: 8.7548
Evaluate side-chains
  95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  418 ILE
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0970
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0010
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
E 409 GLN
E 477 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.106189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.087463 restraints weight = 11646.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.090797 restraints weight = 5760.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.093095 restraints weight = 3555.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.094641 restraints weight = 2514.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.095713 restraints weight = 1956.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6714  Z= 0.111
  Angle     :  0.624  20.633   9148  Z= 0.283
  Chirality :  0.044   0.298    986
  Planarity :  0.004   0.055   1161
  Dihedral  :  7.260  58.634   1140
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.64 %
    Favored  : 71.57 %
  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 aren not related in a simple way.
  whole: -1.85 (0.29), residues: 774
  helix:  0.14 (0.29), residues: 358
  sheet: -0.85 (0.72), residues: 48
  loop : -2.78 (0.27), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 582 
 TYR   0.010   0.001   TYR A 385 
 PHE   0.009   0.001   PHE A 428 
 TRP   0.008   0.001   TRP E 436 
 HIS   0.002   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6695)
  covalent geometry    : angle       0.58943 ( 9097)
  SS BOND              : bond        0.00668 (    6)
  SS BOND              : angle       2.74811 (   12)
  hydrogen bonds       : bond        0.03561 (  243)
  hydrogen bonds       : angle       3.70666 (  666)
  link_BETA1-4         : bond        0.00532 (    6)
  link_BETA1-4         : angle       2.29109 (   18)
  link_NAG-ASN         : bond        0.00482 (    7)
  link_NAG-ASN         : angle       3.20641 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8873 (tmtt) cc_final: 0.8549 (tppt)
REVERT: A   82 MET cc_start: 0.7563 (ttp) cc_final: 0.6480 (tmm)
REVERT: A  201 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7869 (t0)
REVERT: A  249 MET cc_start: 0.8122 (ttp) cc_final: 0.7898 (tmm)
REVERT: A  256 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8848 (mm)
REVERT: A  306 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7625 (tpp-160)
REVERT: A  479 GLU cc_start: 0.8513 (tp30) cc_final: 0.8230 (tp30)
REVERT: A  557 MET cc_start: 0.9049 (tmm) cc_final: 0.8753 (tmm)
REVERT: E  414 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8945 (tp40)
REVERT: E  428 ASP cc_start: 0.8096 (p0) cc_final: 0.7846 (t0)
REVERT: E  466 ARG cc_start: 0.8386 (ptm160) cc_final: 0.8129 (ptm160)
  outliers start: 26
  outliers final: 17
  residues processed: 96
  average time/residue: 0.0588
  time to fit residues: 8.1364
Evaluate side-chains
  93 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 34 optimal weight:    0.1980
   overall best weight:    0.9986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.105140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.086582 restraints weight = 11682.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.089795 restraints weight = 5822.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.092043 restraints weight = 3637.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.093487 restraints weight = 2588.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.094575 restraints weight = 2038.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6714  Z= 0.147
  Angle     :  0.646  20.781   9148  Z= 0.294
  Chirality :  0.045   0.294    986
  Planarity :  0.004   0.055   1161
  Dihedral  :  7.096  58.587   1137
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.91 %
    Favored  : 71.57 %
  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 aren not related in a simple way.
  whole: -1.71 (0.30), residues: 774
  helix:  0.24 (0.29), residues: 360
  sheet: -0.71 (0.72), residues: 47
  loop : -2.72 (0.28), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.012   0.001   TYR A 183 
 PHE   0.010   0.001   PHE A 327 
 TRP   0.008   0.001   TRP E 436 
 HIS   0.002   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6695)
  covalent geometry    : angle       0.61013 ( 9097)
  SS BOND              : bond        0.00273 (    6)
  SS BOND              : angle       2.24154 (   12)
  hydrogen bonds       : bond        0.03871 (  243)
  hydrogen bonds       : angle       3.73541 (  666)
  link_BETA1-4         : bond        0.00681 (    6)
  link_BETA1-4         : angle       2.41995 (   18)
  link_NAG-ASN         : bond        0.00429 (    7)
  link_NAG-ASN         : angle       3.52051 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 80
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8528 (tppt)
REVERT: A   82 MET cc_start: 0.7589 (ttp) cc_final: 0.6458 (tmm)
REVERT: A  190 MET cc_start: 0.8626 (tmm) cc_final: 0.8308 (ttt)
REVERT: A  201 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.7937 (t0)
REVERT: A  249 MET cc_start: 0.7973 (ttp) cc_final: 0.7742 (tmm)
REVERT: A  306 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7564 (tpp-160)
REVERT: A  479 GLU cc_start: 0.8509 (tp30) cc_final: 0.8225 (tp30)
REVERT: A  557 MET cc_start: 0.9014 (tmm) cc_final: 0.8668 (tmm)
REVERT: E  357 ARG cc_start: 0.7324 (ptm160) cc_final: 0.6992 (ptm-80)
REVERT: E  414 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8897 (tp40)
REVERT: E  428 ASP cc_start: 0.8098 (p0) cc_final: 0.7893 (t0)
  outliers start: 31
  outliers final: 20
  residues processed: 103
  average time/residue: 0.0615
  time to fit residues: 8.9667
Evaluate side-chains
  100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  474 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 23 optimal weight:    9.9990
   overall best weight:    2.0986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.102097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.084119 restraints weight = 11669.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.087306 restraints weight = 5819.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.089479 restraints weight = 3606.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.090962 restraints weight = 2554.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.091982 restraints weight = 1990.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   6714  Z= 0.274
  Angle     :  0.793  26.012   9148  Z= 0.352
  Chirality :  0.051   0.383    986
  Planarity :  0.004   0.056   1161
  Dihedral  :  8.003  58.165   1136
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 23.76 %
    Favored  : 71.57 %
  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 aren not related in a simple way.
  whole: -1.76 (0.30), residues: 774
  helix:  0.23 (0.29), residues: 354
  sheet: -0.87 (0.72), residues: 48
  loop : -2.71 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 457 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.015   0.002   PHE E 400 
 TRP   0.011   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00653 ( 6695)
  covalent geometry    : angle       0.73646 ( 9097)
  SS BOND              : bond        0.00632 (    6)
  SS BOND              : angle       3.65885 (   12)
  hydrogen bonds       : bond        0.04780 (  243)
  hydrogen bonds       : angle       4.00786 (  666)
  link_BETA1-4         : bond        0.00646 (    6)
  link_BETA1-4         : angle       2.95193 (   18)
  link_NAG-ASN         : bond        0.00490 (    7)
  link_NAG-ASN         : angle       4.89146 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 79
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7558 (ttp) cc_final: 0.6479 (tmm)
REVERT: A  156 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8716 (tt)
REVERT: A  190 MET cc_start: 0.8616 (tmm) cc_final: 0.8220 (ttt)
REVERT: A  201 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8113 (t0)
REVERT: A  249 MET cc_start: 0.8131 (ttp) cc_final: 0.7795 (tmm)
REVERT: A  306 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7613 (tpp-160)
REVERT: A  479 GLU cc_start: 0.8551 (tp30) cc_final: 0.8252 (tp30)
REVERT: A  557 MET cc_start: 0.9056 (tmm) cc_final: 0.8709 (tmm)
REVERT: E  357 ARG cc_start: 0.7454 (ptm160) cc_final: 0.7001 (ptm-80)
REVERT: E  414 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8938 (tp40)
  outliers start: 32
  outliers final: 21
  residues processed: 106
  average time/residue: 0.0644
  time to fit residues: 9.5628
Evaluate side-chains
  101 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  306 ARG
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  474 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.105537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.087343 restraints weight = 11539.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.090574 restraints weight = 5785.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.092769 restraints weight = 3601.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.094294 restraints weight = 2562.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.095359 restraints weight = 1994.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6714  Z= 0.119
  Angle     :  0.689  29.341   9148  Z= 0.297
  Chirality :  0.046   0.299    986
  Planarity :  0.004   0.056   1161
  Dihedral  :  8.352  81.023   1136
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 24.34 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.30), residues: 774
  helix:  0.36 (0.29), residues: 360
  sheet: -0.78 (0.72), residues: 49
  loop : -2.65 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.011   0.001   TYR A 385 
 PHE   0.010   0.001   PHE A 327 
 TRP   0.009   0.001   TRP A 163 
 HIS   0.005   0.001   HIS E 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6695)
  covalent geometry    : angle       0.66444 ( 9097)
  SS BOND              : bond        0.00394 (    6)
  SS BOND              : angle       2.84062 (   12)
  hydrogen bonds       : bond        0.03774 (  243)
  hydrogen bonds       : angle       3.73896 (  666)
  link_BETA1-4         : bond        0.00416 (    6)
  link_BETA1-4         : angle       2.70577 (   18)
  link_NAG-ASN         : bond        0.00680 (    7)
  link_NAG-ASN         : angle       2.11177 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8875 (tmtt) cc_final: 0.8490 (tppt)
REVERT: A  156 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8687 (tt)
REVERT: A  190 MET cc_start: 0.8612 (tmm) cc_final: 0.8194 (ttt)
REVERT: A  201 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7858 (t0)
REVERT: A  249 MET cc_start: 0.8022 (ttp) cc_final: 0.7743 (tmm)
REVERT: A  479 GLU cc_start: 0.8461 (tp30) cc_final: 0.8215 (tp30)
REVERT: A  557 MET cc_start: 0.9024 (tmm) cc_final: 0.8671 (tmm)
REVERT: E  357 ARG cc_start: 0.7350 (ptm160) cc_final: 0.6908 (ptm-80)
REVERT: E  417 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7334 (t0)
  outliers start: 29
  outliers final: 20
  residues processed: 106
  average time/residue: 0.0659
  time to fit residues: 9.8977
Evaluate side-chains
  102 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  474 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.2984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.103920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.085713 restraints weight = 11678.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.088878 restraints weight = 5892.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.091054 restraints weight = 3688.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.092533 restraints weight = 2637.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.093582 restraints weight = 2067.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6714  Z= 0.180
  Angle     :  0.715  27.976   9148  Z= 0.316
  Chirality :  0.047   0.296    986
  Planarity :  0.004   0.055   1161
  Dihedral  :  6.795  58.200   1130
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 23.32 %
    Favored  : 72.01 %
  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 aren not related in a simple way.
  whole: -1.55 (0.30), residues: 774
  helix:  0.40 (0.29), residues: 360
  sheet: -0.64 (0.72), residues: 48
  loop : -2.67 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 457 
 TYR   0.013   0.001   TYR A 385 
 PHE   0.012   0.001   PHE A 327 
 TRP   0.008   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 6695)
  covalent geometry    : angle       0.68301 ( 9097)
  SS BOND              : bond        0.00560 (    6)
  SS BOND              : angle       3.01375 (   12)
  hydrogen bonds       : bond        0.04258 (  243)
  hydrogen bonds       : angle       3.84242 (  666)
  link_BETA1-4         : bond        0.00394 (    6)
  link_BETA1-4         : angle       2.56670 (   18)
  link_NAG-ASN         : bond        0.00397 (    7)
  link_NAG-ASN         : angle       3.09509 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8944 (tmtt) cc_final: 0.8550 (tppt)
REVERT: A  156 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8731 (tt)
REVERT: A  190 MET cc_start: 0.8600 (tmm) cc_final: 0.8197 (ttt)
REVERT: A  201 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7989 (t0)
REVERT: A  249 MET cc_start: 0.8099 (ttp) cc_final: 0.7798 (tmm)
REVERT: A  474 MET cc_start: 0.8987 (mmm) cc_final: 0.8512 (mmp)
REVERT: A  479 GLU cc_start: 0.8557 (tp30) cc_final: 0.8261 (tp30)
REVERT: A  557 MET cc_start: 0.9039 (tmm) cc_final: 0.8685 (tmm)
REVERT: E  357 ARG cc_start: 0.7407 (ptm160) cc_final: 0.6966 (ptm-80)
REVERT: E  414 GLN cc_start: 0.9208 (tp40) cc_final: 0.8965 (tp40)
REVERT: E  417 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7250 (t0)
REVERT: E  428 ASP cc_start: 0.8123 (p0) cc_final: 0.7887 (t0)
  outliers start: 32
  outliers final: 22
  residues processed: 104
  average time/residue: 0.0590
  time to fit residues: 8.6397
Evaluate side-chains
  102 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  420 ASP
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  474 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.7982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.106195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.087754 restraints weight = 11493.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.091005 restraints weight = 5763.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.093236 restraints weight = 3599.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.094779 restraints weight = 2560.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.095856 restraints weight = 1994.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6714  Z= 0.131
  Angle     :  0.683  29.269   9148  Z= 0.301
  Chirality :  0.044   0.298    986
  Planarity :  0.004   0.055   1161
  Dihedral  :  6.529  58.282   1130
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.05 %
    Favored  : 72.16 %
  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 aren not related in a simple way.
  whole: -1.43 (0.30), residues: 774
  helix:  0.47 (0.29), residues: 366
  sheet: -0.50 (0.74), residues: 48
  loop : -2.64 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.011   0.001   TYR A 183 
 PHE   0.010   0.001   PHE A 327 
 TRP   0.010   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6695)
  covalent geometry    : angle       0.65684 ( 9097)
  SS BOND              : bond        0.00521 (    6)
  SS BOND              : angle       2.90548 (   12)
  hydrogen bonds       : bond        0.03801 (  243)
  hydrogen bonds       : angle       3.74282 (  666)
  link_BETA1-4         : bond        0.00471 (    6)
  link_BETA1-4         : angle       2.38688 (   18)
  link_NAG-ASN         : bond        0.00501 (    7)
  link_NAG-ASN         : angle       2.60932 (   21)

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

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

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1548 Ramachandran restraints generated.
    774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8910 (tmtt) cc_final: 0.8540 (tppt)
REVERT: A  190 MET cc_start: 0.8600 (tmm) cc_final: 0.8183 (ttt)
REVERT: A  201 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8001 (t0)
REVERT: A  208 GLU cc_start: 0.8259 (tt0) cc_final: 0.8037 (tt0)
REVERT: A  249 MET cc_start: 0.7994 (ttp) cc_final: 0.7747 (tmm)
REVERT: A  474 MET cc_start: 0.8947 (mmm) cc_final: 0.8636 (mmp)
REVERT: A  479 GLU cc_start: 0.8493 (tp30) cc_final: 0.8209 (tp30)
REVERT: A  557 MET cc_start: 0.9023 (tmm) cc_final: 0.8666 (tmm)
REVERT: E  357 ARG cc_start: 0.7363 (ptm160) cc_final: 0.6934 (ptm-80)
REVERT: E  406 GLU cc_start: 0.8704 (tt0) cc_final: 0.8493 (tt0)
REVERT: E  414 GLN cc_start: 0.9162 (tp40) cc_final: 0.8909 (tp40)
REVERT: E  417 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7545 (t0)
  outliers start: 26
  outliers final: 21
  residues processed: 107
  average time/residue: 0.0547
  time to fit residues: 8.4001
Evaluate side-chains
  103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain E residue  369 TYR
Chi-restraints excluded: chain E residue  382 VAL
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  395 VAL
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  420 ASP
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Chi-restraints excluded: chain E residue  474 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0030
   chunk 23 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0050
   overall best weight:    0.5804

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.112752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.094665 restraints weight = 11401.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.097912 restraints weight = 5770.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.100136 restraints weight = 3605.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.101532 restraints weight = 2564.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.102609 restraints weight = 2026.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6714  Z= 0.115
  Angle     :  0.672  29.908   9148  Z= 0.298
  Chirality :  0.044   0.296    986
  Planarity :  0.004   0.055   1161
  Dihedral  :  6.280  58.422   1130
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 25.36 %
    Favored  : 71.57 %
  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 aren not related in a simple way.
  whole: -1.28 (0.30), residues: 774
  helix:  0.59 (0.29), residues: 366
  sheet: -0.42 (0.76), residues: 49
  loop : -2.55 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.010   0.001   TYR A 183 
 PHE   0.013   0.001   PHE E 429 
 TRP   0.009   0.001   TRP E 436 
 HIS   0.002   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6695)
  covalent geometry    : angle       0.64837 ( 9097)
  SS BOND              : bond        0.00373 (    6)
  SS BOND              : angle       2.83763 (   12)
  hydrogen bonds       : bond        0.03463 (  243)
  hydrogen bonds       : angle       3.68410 (  666)
  link_BETA1-4         : bond        0.00472 (    6)
  link_BETA1-4         : angle       2.25346 (   18)
  link_NAG-ASN         : bond        0.00466 (    7)
  link_NAG-ASN         : angle       2.35923 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1027.46 seconds
wall clock time: 18 minutes 24.50 seconds (1104.50 seconds total)