Starting phenix.real_space_refine
on Thu Jul 24 19:25:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i9h_35272/07_2025/8i9h_35272.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i9h_35272/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i9h_35272/07_2025/8i9h_35272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i9h_35272/07_2025/8i9h_35272.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i9h_35272/07_2025/8i9h_35272.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i9h_35272/07_2025/8i9h_35272.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.76, per 1000 atoms: 0.73
  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: 1.98
  Conformation dependent library (CDL) restraints added in 931.4 milliseconds
  

  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: 0.74
  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: 1.73

  Time building geometry restraints manager: 2.29 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:             2.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     21.410
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.450
-------------------------------------------------------------------------------
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 : 8.35
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.010   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.012   0.002   PHE E 400 
 TYR   0.017   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 169 

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

*********************** 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  : 0.773 
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: 0.1929
  time to fit residues: 34.5476
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  : 0.774 
-------------------------------------------------------------------------------
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 65 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0570
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 60 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0010
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.4104

-------------------------------------------------------------------------------
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 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: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.103868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.085844 restraints weight = 11231.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.089147 restraints weight = 5475.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.091421 restraints weight = 3342.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1238

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= 0.117
  Angle     :  0.646  14.091   9148  Z= 0.306
  Chirality :  0.045   0.323    986
  Planarity :  0.004   0.059   1161
  Dihedral  :  9.550  58.841   1192
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 21.72 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.10 (0.27), residues: 774
  helix: -0.99 (0.27), residues: 363
  sheet: -1.54 (0.67), residues: 49
  loop : -3.36 (0.26), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 265 
 PHE   0.013   0.001   PHE A 428 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00662 (    7)
  link_NAG-ASN         : angle       3.16719 (   21)
  link_BETA1-4         : bond        0.00493 (    6)
  link_BETA1-4         : angle       2.42104 (   18)
  hydrogen bonds       : bond        0.04500 (  243)
  hydrogen bonds       : angle       4.21047 (  666)
  SS BOND              : bond        0.00688 (    6)
  SS BOND              : angle       1.48826 (   12)
  covalent geometry    : bond        0.00253 ( 6695)
  covalent geometry    : angle       0.61782 ( 9097)

*********************** 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
  118 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 80
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8455 (tptp)
REVERT: A   82 MET cc_start: 0.7793 (ttp) cc_final: 0.6928 (tmm)
REVERT: A  201 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8159 (t70)
REVERT: A  340 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7552 (mm110)
REVERT: A  474 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8505 (mmm)
REVERT: E  414 GLN cc_start: 0.9268 (mm-40) cc_final: 0.9022 (tp40)
REVERT: E  466 ARG cc_start: 0.8347 (ptm160) cc_final: 0.8049 (ptm160)
  outliers start: 38
  outliers final: 20
  residues processed: 110
  average time/residue: 0.1498
  time to fit residues: 23.2352
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
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 76 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0370
   chunk 61 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6858

-------------------------------------------------------------------------------
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
E 487 ASN
** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.105309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.086879 restraints weight = 11540.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.090148 restraints weight = 5745.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.092375 restraints weight = 3563.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.1426

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= 0.121
  Angle     :  0.612  14.774   9148  Z= 0.288
  Chirality :  0.045   0.297    986
  Planarity :  0.004   0.057   1161
  Dihedral  :  7.999  59.881   1143
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.03 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.28), residues: 774
  helix: -0.44 (0.28), residues: 363
  sheet: -1.35 (0.69), residues: 49
  loop : -3.10 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.011   0.001   PHE A 428 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.001   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00487 (    7)
  link_NAG-ASN         : angle       2.70255 (   21)
  link_BETA1-4         : bond        0.00467 (    6)
  link_BETA1-4         : angle       2.28828 (   18)
  hydrogen bonds       : bond        0.04018 (  243)
  hydrogen bonds       : angle       3.96878 (  666)
  SS BOND              : bond        0.00512 (    6)
  SS BOND              : angle       2.20375 (   12)
  covalent geometry    : bond        0.00277 ( 6695)
  covalent geometry    : angle       0.58538 ( 9097)

*********************** 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
  105 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8418 (tptp)
REVERT: A   82 MET cc_start: 0.7787 (ttp) cc_final: 0.6858 (tmm)
REVERT: A  201 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8090 (t0)
REVERT: A  249 MET cc_start: 0.8226 (ttp) cc_final: 0.7958 (tmm)
REVERT: A  306 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7191 (tpp-160)
REVERT: A  323 MET cc_start: 0.8125 (mmm) cc_final: 0.7830 (mmm)
REVERT: A  340 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7684 (mm110)
REVERT: A  479 GLU cc_start: 0.8443 (tp30) cc_final: 0.8232 (tp30)
REVERT: E  414 GLN cc_start: 0.9263 (mm-40) cc_final: 0.9012 (tp40)
  outliers start: 29
  outliers final: 19
  residues processed: 101
  average time/residue: 0.1549
  time to fit residues: 22.3912
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
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 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  430 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0870
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
E 409 GLN
E 477 ASN
E 487 ASN
E 493 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.105306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.086814 restraints weight = 11622.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.090087 restraints weight = 5802.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.092324 restraints weight = 3601.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1621

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= 0.129
  Angle     :  0.606  15.221   9148  Z= 0.284
  Chirality :  0.044   0.296    986
  Planarity :  0.004   0.056   1161
  Dihedral  :  7.653  58.695   1140
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 23.76 %
    Favored  : 71.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.29), residues: 774
  helix: -0.12 (0.29), residues: 359
  sheet: -1.19 (0.70), residues: 49
  loop : -2.95 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.003   0.001   HIS A 241 
 PHE   0.010   0.001   PHE A 327 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.001   0.000   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00505 (    7)
  link_NAG-ASN         : angle       2.76684 (   21)
  link_BETA1-4         : bond        0.00512 (    6)
  link_BETA1-4         : angle       2.31516 (   18)
  hydrogen bonds       : bond        0.03879 (  243)
  hydrogen bonds       : angle       3.85699 (  666)
  SS BOND              : bond        0.00269 (    6)
  SS BOND              : angle       2.06279 (   12)
  covalent geometry    : bond        0.00302 ( 6695)
  covalent geometry    : angle       0.57954 ( 9097)

*********************** 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
  114 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 80
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8673 (tppt)
REVERT: A   82 MET cc_start: 0.7654 (ttp) cc_final: 0.6641 (tmm)
REVERT: A  201 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8018 (t0)
REVERT: A  249 MET cc_start: 0.8182 (ttp) cc_final: 0.7907 (tmm)
REVERT: A  306 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7450 (tpp-160)
REVERT: A  479 GLU cc_start: 0.8510 (tp30) cc_final: 0.8244 (tp30)
REVERT: E  414 GLN cc_start: 0.9260 (mm-40) cc_final: 0.8991 (tp40)
REVERT: E  442 ASP cc_start: 0.8485 (m-30) cc_final: 0.8263 (t0)
REVERT: E  466 ARG cc_start: 0.8267 (ptm160) cc_final: 0.8054 (ptm160)
  outliers start: 34
  outliers final: 21
  residues processed: 110
  average time/residue: 0.1470
  time to fit residues: 23.0228
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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  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  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  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 61 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0070
   chunk 40 optimal weight:    0.1980
   chunk 6 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 45 optimal weight:    0.3980
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.4198

-------------------------------------------------------------------------------
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 = 0.3275 r_free = 0.3275 target = 0.107244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.088621 restraints weight = 11479.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.091937 restraints weight = 5726.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.094198 restraints weight = 3545.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6714  Z= 0.100
  Angle     :  0.638  25.830   9148  Z= 0.279
  Chirality :  0.043   0.297    986
  Planarity :  0.004   0.054   1161
  Dihedral  :  7.128  58.783   1140
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 24.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.29), residues: 774
  helix:  0.17 (0.29), residues: 359
  sheet: -0.83 (0.71), residues: 48
  loop : -2.74 (0.27), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.002   0.001   HIS A 265 
 PHE   0.010   0.001   PHE E 342 
 TYR   0.009   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00595 (    7)
  link_NAG-ASN         : angle       3.26029 (   21)
  link_BETA1-4         : bond        0.00565 (    6)
  link_BETA1-4         : angle       2.24328 (   18)
  hydrogen bonds       : bond        0.03341 (  243)
  hydrogen bonds       : angle       3.68555 (  666)
  SS BOND              : bond        0.00595 (    6)
  SS BOND              : angle       2.51496 (   12)
  covalent geometry    : bond        0.00219 ( 6695)
  covalent geometry    : angle       0.60534 ( 9097)

*********************** 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
  109 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8876 (tmtt) cc_final: 0.8582 (tppt)
REVERT: A   82 MET cc_start: 0.7605 (ttp) cc_final: 0.6566 (tmm)
REVERT: A  101 GLN cc_start: 0.8739 (tt0) cc_final: 0.8498 (tt0)
REVERT: A  201 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.7896 (t0)
REVERT: A  479 GLU cc_start: 0.8501 (tp30) cc_final: 0.8220 (tp30)
REVERT: A  557 MET cc_start: 0.9026 (tmm) cc_final: 0.8731 (tmm)
REVERT: E  414 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8965 (tp40)
REVERT: E  428 ASP cc_start: 0.8089 (p0) cc_final: 0.7866 (t0)
REVERT: E  466 ARG cc_start: 0.8277 (ptm160) cc_final: 0.8074 (ptm160)
  outliers start: 25
  outliers final: 19
  residues processed: 102
  average time/residue: 0.1516
  time to fit residues: 21.8183
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
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  123 MET
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  201 ASP
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  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  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 10 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0170
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7220

-------------------------------------------------------------------------------
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 = 0.3265 r_free = 0.3265 target = 0.106376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.088000 restraints weight = 11370.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.091267 restraints weight = 5657.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.093495 restraints weight = 3511.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6714  Z= 0.120
  Angle     :  0.646  24.513   9148  Z= 0.287
  Chirality :  0.044   0.293    986
  Planarity :  0.004   0.054   1161
  Dihedral  :  6.744  58.828   1133
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 23.62 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.29), residues: 774
  helix:  0.32 (0.29), residues: 359
  sheet: -0.73 (0.72), residues: 48
  loop : -2.68 (0.28), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 436 
 HIS   0.002   0.000   HIS A 241 
 PHE   0.009   0.001   PHE A 327 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00438 (    7)
  link_NAG-ASN         : angle       3.63955 (   21)
  link_BETA1-4         : bond        0.00704 (    6)
  link_BETA1-4         : angle       2.33564 (   18)
  hydrogen bonds       : bond        0.03551 (  243)
  hydrogen bonds       : angle       3.68273 (  666)
  SS BOND              : bond        0.00372 (    6)
  SS BOND              : angle       2.48382 (   12)
  covalent geometry    : bond        0.00276 ( 6695)
  covalent geometry    : angle       0.60857 ( 9097)

*********************** 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
  108 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8903 (tmtt) cc_final: 0.8589 (tppt)
REVERT: A   82 MET cc_start: 0.7586 (ttp) cc_final: 0.6490 (tmm)
REVERT: A  101 GLN cc_start: 0.8738 (tt0) cc_final: 0.8510 (tt0)
REVERT: A  201 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.7906 (t0)
REVERT: A  293 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7509 (m)
REVERT: A  479 GLU cc_start: 0.8490 (tp30) cc_final: 0.8193 (tp30)
REVERT: A  557 MET cc_start: 0.9000 (tmm) cc_final: 0.8672 (tmm)
REVERT: E  406 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8427 (tt0)
REVERT: E  414 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8949 (tp40)
  outliers start: 26
  outliers final: 16
  residues processed: 99
  average time/residue: 0.1451
  time to fit residues: 20.7648
Evaluate side-chains
  97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
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  141 CYS
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  293 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  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  406 GLU
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 24 optimal weight:    0.0980
   chunk 13 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3312 r_free = 0.3312 target = 0.109077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.090247 restraints weight = 11456.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.093528 restraints weight = 5820.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.095802 restraints weight = 3662.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6714  Z= 0.114
  Angle     :  0.676  25.222   9148  Z= 0.289
  Chirality :  0.045   0.400    986
  Planarity :  0.004   0.054   1161
  Dihedral  :  7.154  58.848   1128
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.30), residues: 774
  helix:  0.45 (0.29), residues: 359
  sheet: -0.60 (0.73), residues: 48
  loop : -2.57 (0.28), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.002   0.001   HIS A 241 
 PHE   0.009   0.001   PHE A 327 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.001   0.000   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00623 (    7)
  link_NAG-ASN         : angle       5.03763 (   21)
  link_BETA1-4         : bond        0.00703 (    6)
  link_BETA1-4         : angle       2.53691 (   18)
  hydrogen bonds       : bond        0.03428 (  243)
  hydrogen bonds       : angle       3.63117 (  666)
  SS BOND              : bond        0.00269 (    6)
  SS BOND              : angle       2.36987 (   12)
  covalent geometry    : bond        0.00257 ( 6695)
  covalent geometry    : angle       0.61750 ( 9097)

*********************** 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
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8614 (tppt)
REVERT: A   82 MET cc_start: 0.7564 (ttp) cc_final: 0.6516 (tmm)
REVERT: A  101 GLN cc_start: 0.8682 (tt0) cc_final: 0.8448 (tt0)
REVERT: A  201 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.7876 (t0)
REVERT: A  479 GLU cc_start: 0.8471 (tp30) cc_final: 0.8227 (tp30)
REVERT: E  414 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8919 (tp40)
  outliers start: 22
  outliers final: 15
  residues processed: 93
  average time/residue: 0.1457
  time to fit residues: 19.9956
Evaluate side-chains
  94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
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  141 CYS
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
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  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  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 12 optimal weight:    0.0770
   chunk 31 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.1980
   chunk 36 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.3314 r_free = 0.3314 target = 0.109416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.090724 restraints weight = 11484.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.094005 restraints weight = 5772.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.096288 restraints weight = 3615.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6714  Z= 0.103
  Angle     :  0.641  24.638   9148  Z= 0.280
  Chirality :  0.044   0.291    986
  Planarity :  0.004   0.054   1161
  Dihedral  :  7.256  69.680   1126
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 23.03 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.30), residues: 774
  helix:  0.59 (0.29), residues: 359
  sheet: -0.65 (0.72), residues: 49
  loop : -2.50 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.004   0.001   HIS E 339 
 PHE   0.008   0.001   PHE A 428 
 TYR   0.009   0.001   TYR A 385 
 ARG   0.001   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00600 (    7)
  link_NAG-ASN         : angle       2.09218 (   21)
  link_BETA1-4         : bond        0.00456 (    6)
  link_BETA1-4         : angle       2.54731 (   18)
  hydrogen bonds       : bond        0.03289 (  243)
  hydrogen bonds       : angle       3.59067 (  666)
  SS BOND              : bond        0.00220 (    6)
  SS BOND              : angle       2.30956 (   12)
  covalent geometry    : bond        0.00230 ( 6695)
  covalent geometry    : angle       0.61900 ( 9097)

*********************** 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
  109 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8904 (tmtt) cc_final: 0.8593 (tppt)
REVERT: A   82 MET cc_start: 0.7567 (ttp) cc_final: 0.6598 (tmm)
REVERT: A  201 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7886 (t0)
REVERT: A  479 GLU cc_start: 0.8507 (tp30) cc_final: 0.8211 (tp30)
REVERT: A  557 MET cc_start: 0.8994 (tmm) cc_final: 0.8710 (tmm)
REVERT: E  406 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8438 (tt0)
  outliers start: 27
  outliers final: 18
  residues processed: 101
  average time/residue: 0.1359
  time to fit residues: 20.1841
Evaluate side-chains
  97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
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  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 A residue  558 LEU
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  406 GLU
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0010
   chunk 13 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.109241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.090406 restraints weight = 11599.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.093705 restraints weight = 5848.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.095964 restraints weight = 3664.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2256

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= 0.113
  Angle     :  0.642  25.345   9148  Z= 0.285
  Chirality :  0.044   0.292    986
  Planarity :  0.004   0.053   1161
  Dihedral  :  5.895  58.943   1126
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.76 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.30), residues: 774
  helix:  0.68 (0.29), residues: 365
  sheet: -0.48 (0.73), residues: 49
  loop : -2.49 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.009   0.001   PHE A 327 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.001   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00433 (    7)
  link_NAG-ASN         : angle       2.79397 (   21)
  link_BETA1-4         : bond        0.00416 (    6)
  link_BETA1-4         : angle       2.18778 (   18)
  hydrogen bonds       : bond        0.03387 (  243)
  hydrogen bonds       : angle       3.60734 (  666)
  SS BOND              : bond        0.00201 (    6)
  SS BOND              : angle       2.57744 (   12)
  covalent geometry    : bond        0.00256 ( 6695)
  covalent geometry    : angle       0.61536 ( 9097)

*********************** 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
  103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.752 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8921 (tmtt) cc_final: 0.8613 (tppt)
REVERT: A   82 MET cc_start: 0.7586 (ttp) cc_final: 0.6608 (tmm)
REVERT: A  201 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7902 (t0)
REVERT: A  278 LEU cc_start: 0.9300 (mt) cc_final: 0.8950 (mt)
REVERT: A  479 GLU cc_start: 0.8491 (tp30) cc_final: 0.8249 (tp30)
REVERT: A  557 MET cc_start: 0.9003 (tmm) cc_final: 0.8705 (tmm)
REVERT: E  406 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8462 (tt0)
REVERT: E  417 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7535 (t0)
  outliers start: 22
  outliers final: 15
  residues processed: 98
  average time/residue: 0.1637
  time to fit residues: 23.2561
Evaluate side-chains
  98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  201 ASP
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  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  558 LEU
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  406 GLU
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    0.4980
   chunk 73 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0270
   chunk 32 optimal weight:    0.1980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.110183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.091468 restraints weight = 11509.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.094798 restraints weight = 5802.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.097085 restraints weight = 3619.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6714  Z= 0.104
  Angle     :  0.636  26.104   9148  Z= 0.283
  Chirality :  0.043   0.293    986
  Planarity :  0.004   0.054   1161
  Dihedral  :  5.732  58.913   1126
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 23.76 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.30), residues: 774
  helix:  0.78 (0.29), residues: 365
  sheet: -0.34 (0.77), residues: 49
  loop : -2.42 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 436 
 HIS   0.003   0.001   HIS E 339 
 PHE   0.007   0.001   PHE A 327 
 TYR   0.009   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00442 (    7)
  link_NAG-ASN         : angle       2.41266 (   21)
  link_BETA1-4         : bond        0.00457 (    6)
  link_BETA1-4         : angle       2.13279 (   18)
  hydrogen bonds       : bond        0.03189 (  243)
  hydrogen bonds       : angle       3.57008 (  666)
  SS BOND              : bond        0.00170 (    6)
  SS BOND              : angle       2.39029 (   12)
  covalent geometry    : bond        0.00232 ( 6695)
  covalent geometry    : angle       0.61400 ( 9097)

********************** 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
  102 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.612 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8584 (tppt)
REVERT: A   82 MET cc_start: 0.7623 (ttp) cc_final: 0.6610 (tmm)
REVERT: A  201 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7826 (t0)
REVERT: A  208 GLU cc_start: 0.8274 (tt0) cc_final: 0.8056 (tt0)
REVERT: A  278 LEU cc_start: 0.9283 (mt) cc_final: 0.8953 (mt)
REVERT: A  479 GLU cc_start: 0.8525 (tp30) cc_final: 0.8264 (tp30)
REVERT: A  557 MET cc_start: 0.9002 (tmm) cc_final: 0.8708 (tmm)
REVERT: E  406 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8456 (tt0)
REVERT: E  414 GLN cc_start: 0.9175 (tp40) cc_final: 0.8899 (tp40)
REVERT: E  417 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7550 (t0)
  outliers start: 24
  outliers final: 17
  residues processed: 97
  average time/residue: 0.1949
  time to fit residues: 27.9791
Evaluate side-chains
  94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASP
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  316 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain E residue  367 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  406 GLU
Chi-restraints excluded: chain E residue  417 ASN
Chi-restraints excluded: chain E residue  430 THR
Chi-restraints excluded: chain E residue  452 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 7 optimal weight:    0.4980
   chunk 72 optimal weight:    0.0470
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0370
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.3756

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.110656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.091923 restraints weight = 11599.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.095288 restraints weight = 5824.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.097568 restraints weight = 3629.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6714  Z= 0.100
  Angle     :  0.633  25.888   9148  Z= 0.283
  Chirality :  0.043   0.292    986
  Planarity :  0.004   0.053   1161
  Dihedral  :  5.609  58.993   1126
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.34 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.30), residues: 774
  helix:  0.87 (0.28), residues: 365
  sheet: -0.27 (0.78), residues: 49
  loop : -2.37 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 436 
 HIS   0.002   0.001   HIS A 417 
 PHE   0.008   0.001   PHE A 327 
 TYR   0.009   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00457 (    7)
  link_NAG-ASN         : angle       2.29701 (   21)
  link_BETA1-4         : bond        0.00460 (    6)
  link_BETA1-4         : angle       2.07920 (   18)
  hydrogen bonds       : bond        0.03036 (  243)
  hydrogen bonds       : angle       3.52011 (  666)
  SS BOND              : bond        0.00161 (    6)
  SS BOND              : angle       2.22507 (   12)
  covalent geometry    : bond        0.00219 ( 6695)
  covalent geometry    : angle       0.61247 ( 9097)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2380.78 seconds
wall clock time: 42 minutes 45.67 seconds (2565.67 seconds total)