Starting phenix.real_space_refine
on Sun Apr 27 21:50:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y32_38866/04_2025/8y32_38866.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y32_38866/04_2025/8y32_38866.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y32_38866/04_2025/8y32_38866.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y32_38866/04_2025/8y32_38866.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y32_38866/04_2025/8y32_38866.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y32_38866/04_2025/8y32_38866.cif"
  }
  resolution = 4.13
  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=   0.001 sd=   0.070
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     Cl      1      4.86       5
     C    4207      2.51       5
     N    1084      2.21       5
     O    1241      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6571
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4906
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 571}
    Chain: "B"
      Number of atoms: 1566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1566
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 13, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {' CL': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    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
  Time building chain proxies: 4.55, per 1000 atoms: 0.69
  Number of scatterers: 6571
  At special positions: 0
  Unit cell: (93.09, 85.6, 126.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      38     16.00
     O    1241      8.00
     N    1084      7.00
     C    4207      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 902 " - " ASN A  53 "
      " NAG A 903 " - " ASN A  90 "
      " NAG A 905 " - " ASN A 431 "
      " NAG A 906 " - " ASN A 545 "
      " NAG B 601 " - " ASN B 343 "
      " NAG B 602 " - " ASN B 354 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 957.3 milliseconds
  

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      50.9% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 36
    Processing helix  chain 'A' and resid 37 through 51
      removed outlier: 3.606A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.574A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   TRP A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   PHE A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER A  77 " --> pdb=" O   TYR A  73 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ARG A  78 " --> pdb=" O   GLU A  74 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   MET A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.638A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA A  99 " --> pdb=" O   ARG A  95 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU A 100 " --> pdb=" O   GLN A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 115
    Processing helix  chain 'A' and resid 115 through 129
    Processing helix  chain 'A' and resid 145 through 154
    Processing helix  chain 'A' and resid 157 through 165
    Processing helix  chain 'A' and resid 166 through 191
      removed outlier: 4.681A  pdb=" N   GLY A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   LYS A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
      removed outlier: 3.717A  pdb=" N   VAL A 184 " --> pdb=" O   GLU A 180 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   MET A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ALA A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ARG A 191 " --> pdb=" O   ASN A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 197 through 204
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.547A  pdb=" N   LEU A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   MET A 222 " --> pdb=" O   ARG A 218 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LYS A 223 " --> pdb=" O   ASP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 251
      removed outlier: 3.519A  pdb=" N   HIS A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 3.564A  pdb=" N   ILE A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   PHE A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 327
    Processing helix  chain 'A' and resid 364 through 384
      removed outlier: 3.911A  pdb=" N   TYR A 384 " --> pdb=" O   TYR A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
    Processing helix  chain 'A' and resid 398 through 411
      removed outlier: 3.576A  pdb=" N   ALA A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   MET A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   SER A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 420
    Processing helix  chain 'A' and resid 430 through 446
      removed outlier: 3.763A  pdb=" N   THR A 444 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 464
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.646A  pdb=" N   TRP A 476 " --> pdb=" O   TRP A 472 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLU A 482 " --> pdb=" O   GLU A 478 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ILE A 483 " --> pdb=" O   MET A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 501
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 511 through 532
      removed outlier: 3.974A  pdb=" N   TYR A 515 " --> pdb=" O   PHE A 511 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   THR A 518 " --> pdb=" O   TYR A 514 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ILE A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLU A 526 " --> pdb=" O   PHE A 522 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR A 531 " --> pdb=" O   ALA A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 558
      removed outlier: 3.681A  pdb=" N   MET A 556 " --> pdb=" O   ARG A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 573
      removed outlier: 3.556A  pdb=" N   ALA A 568 " --> pdb=" O   PRO A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 587
      removed outlier: 3.651A  pdb=" N   TYR A 586 " --> pdb=" O   PRO A 582 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 598
      removed outlier: 3.589A  pdb=" N   GLU A 596 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 341
      removed outlier: 4.009A  pdb=" N   GLU B 340 " --> pdb=" O   CYS B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 3.960A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ASP B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 385 through 389'
    Processing helix  chain 'B' and resid 407 through 411
      removed outlier: 3.613A  pdb=" N   ALA B 411 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
      removed outlier: 3.508A  pdb=" N   GLN B 506 " --> pdb=" O   VAL B 503 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 262
      removed outlier: 6.223A  pdb=" N   LEU A 261 " --> pdb=" O   VAL A 487 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348
      removed outlier: 3.553A  pdb=" N   LYS A 358 " --> pdb=" O   THR A 346 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ARG A 356 " --> pdb=" O   TRP A 348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 356 through 358
      removed outlier: 4.199A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 392
      removed outlier: 3.512A  pdb=" N   VAL B 524 " --> pdb=" O   PHE B 392 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474
      removed outlier: 3.618A  pdb=" N   TYR B 473 " --> pdb=" O   TYR B 489 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR B 489 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    240 hydrogen bonds defined for protein.
    672 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: 1.70

  Time building geometry restraints manager: 1.91 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: 2063
        1.34 -     1.46: 1758
        1.46 -     1.58: 2878
        1.58 -     1.71: 0
        1.71 -     1.83: 60
  Bond restraints: 6759
  Sorted by residual:
  bond pdb=" C   TYR A  83 "
       pdb=" N   SER A  84 "
    ideal  model  delta    sigma   weight residual
    1.330  1.450 -0.120 1.31e-02 5.83e+03 8.41e+01
  bond pdb=" C   THR A  82 "
       pdb=" N   TYR A  83 "
    ideal  model  delta    sigma   weight residual
    1.331  1.433 -0.103 1.45e-02 4.76e+03 5.04e+01
  bond pdb=" C   TYR B 489 "
       pdb=" N   PHE B 490 "
    ideal  model  delta    sigma   weight residual
    1.331  1.417 -0.087 1.24e-02 6.50e+03 4.90e+01
  bond pdb=" C   CYS B 488 "
       pdb=" N   TYR B 489 "
    ideal  model  delta    sigma   weight residual
    1.329  1.244  0.085 1.76e-02 3.23e+03 2.35e+01
  bond pdb=" C4  NAG B 602 "
       pdb=" C5  NAG B 602 "
    ideal  model  delta    sigma   weight residual
    1.532  1.499  0.033 2.00e-02 2.50e+03 2.75e+00
  ... (remaining 6754 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 8988
        2.00 -     4.00: 137
        4.00 -     5.99: 33
        5.99 -     7.99: 12
        7.99 -     9.99: 4
  Bond angle restraints: 9174
  Sorted by residual:
  angle pdb=" CA  TYR B 489 "
        pdb=" C   TYR B 489 "
        pdb=" N   PHE B 490 "
      ideal   model   delta    sigma   weight residual
     115.90  123.10   -7.20 1.21e+00 6.83e-01 3.54e+01
  angle pdb=" O   TYR B 489 "
        pdb=" C   TYR B 489 "
        pdb=" N   PHE B 490 "
      ideal   model   delta    sigma   weight residual
     122.59  115.19    7.40 1.35e+00 5.49e-01 3.01e+01
  angle pdb=" C   TYR B 489 "
        pdb=" N   PHE B 490 "
        pdb=" CA  PHE B 490 "
      ideal   model   delta    sigma   weight residual
     122.65  131.50   -8.85 1.66e+00 3.63e-01 2.84e+01
  angle pdb=" CA  TYR A  83 "
        pdb=" C   TYR A  83 "
        pdb=" N   SER A  84 "
      ideal   model   delta    sigma   weight residual
     116.24  122.20   -5.96 1.34e+00 5.57e-01 1.98e+01
  angle pdb=" O   TYR A  83 "
        pdb=" C   TYR A  83 "
        pdb=" N   SER A  84 "
      ideal   model   delta    sigma   weight residual
     123.01  117.19    5.82 1.33e+00 5.65e-01 1.92e+01
  ... (remaining 9169 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.99: 3601
       24.99 -    49.98: 402
       49.98 -    74.97: 43
       74.97 -    99.97: 16
       99.97 -   124.96: 17
  Dihedral angle restraints: 4079
    sinusoidal: 1747
      harmonic: 2332
  Sorted by residual:
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.38   73.62     1      1.00e+01 1.00e-02 6.89e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -15.16  -70.84     1      1.00e+01 1.00e-02 6.45e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.34  -37.34     1      1.00e+01 1.00e-02 1.97e+01
  ... (remaining 4076 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 948
       0.106 -    0.212: 21
       0.212 -    0.318: 0
       0.318 -    0.424: 0
       0.424 -    0.530: 1
  Chirality restraints: 970
  Sorted by residual:
  chirality pdb=" C1  NAG A 902 "
            pdb=" ND2 ASN A  53 "
            pdb=" C2  NAG A 902 "
            pdb=" O5  NAG A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.87   -0.53 2.00e-01 2.50e+01 7.02e+00
  chirality pdb=" C1  NAG B 602 "
            pdb=" ND2 ASN B 354 "
            pdb=" C2  NAG B 602 "
            pdb=" O5  NAG B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.60    0.20 2.00e-01 2.50e+01 9.93e-01
  chirality pdb=" CB  ILE A 255 "
            pdb=" CA  ILE A 255 "
            pdb=" CG1 ILE A 255 "
            pdb=" CG2 ILE A 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.68e-01
  ... (remaining 967 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 601 "    0.308 2.00e-02 2.50e+03   2.69e-01 9.06e+02
        pdb=" C7  NAG B 601 "   -0.064 2.00e-02 2.50e+03
        pdb=" C8  NAG B 601 "    0.039 2.00e-02 2.50e+03
        pdb=" N2  NAG B 601 "   -0.475 2.00e-02 2.50e+03
        pdb=" O7  NAG B 601 "    0.192 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 602 "    0.151 2.00e-02 2.50e+03   1.25e-01 1.95e+02
        pdb=" C7  NAG B 602 "   -0.043 2.00e-02 2.50e+03
        pdb=" C8  NAG B 602 "    0.113 2.00e-02 2.50e+03
        pdb=" N2  NAG B 602 "   -0.200 2.00e-02 2.50e+03
        pdb=" O7  NAG B 602 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 424 "   -0.059 5.00e-02 4.00e+02   8.91e-02 1.27e+01
        pdb=" N   PRO A 425 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO A 425 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 425 "   -0.049 5.00e-02 4.00e+02
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 111
        2.68 -     3.23: 6195
        3.23 -     3.79: 9673
        3.79 -     4.34: 12784
        4.34 -     4.90: 20995
  Nonbonded interactions: 49758
  Sorted by model distance:
  nonbonded pdb=" NE  ARG A 339 "
            pdb=" O7  NAG A 902 "
     model   vdw
     2.120 2.496
  nonbonded pdb=" OD2 ASP A 542 "
            pdb=" OG  SER A 544 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OE1 GLN A 238 "
            pdb=" ND2 ASN A 598 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" ND1 HIS B 339 "
            pdb=" OE1 GLU B 340 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   ASP A 366 "
            pdb=" OG1 THR A 370 "
     model   vdw
     2.278 3.040
  ... (remaining 49753 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.050
  Find NCS groups from input model:        0.060
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120   6771  Z= 0.239
  Angle     :  0.752  14.903   9202  Z= 0.377
  Chirality :  0.046   0.530    970
  Planarity :  0.010   0.269   1169
  Dihedral  : 21.050 124.957   2568
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.48 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 33.29 %
    Favored  : 65.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.08 (0.30), residues: 787
  helix:  0.33 (0.29), residues: 346
  sheet:  0.80 (0.89), residues: 36
  loop : -1.87 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 202 
 HIS   0.004   0.001   HIS A 102 
 PHE   0.012   0.001   PHE B 429 
 TYR   0.009   0.001   TYR A 214 
 ARG   0.003   0.000   ARG A  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01782 (    6)
  link_NAG-ASN         : angle       6.26698 (   18)
  hydrogen bonds       : bond        0.15987 (  240)
  hydrogen bonds       : angle       5.85350 (  672)
  SS BOND              : bond        0.00475 (    5)
  SS BOND              : angle       0.91527 (   10)
  covalent geometry    : bond        0.00426 ( 6759)
  covalent geometry    : angle       0.69917 ( 9174)
  Misc. bond           : bond        0.00014 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A  186 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7368 (tt0)
REVERT: A  254 TYR cc_start: 0.7481 (m-80) cc_final: 0.7182 (m-10)
REVERT: A  381 ASP cc_start: 0.6680 (t0) cc_final: 0.6434 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 117
  average time/residue: 0.1839
  time to fit residues: 28.8379
Evaluate side-chains
  115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0000
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0030
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.3572

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

Flipped N/Q/H residues before XYZ refinement:
A 299 GLN
A 441 GLN
B 439 ASN
B 474 GLN
B 477 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.129249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.126322 restraints weight = 9864.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.126490 restraints weight = 8026.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.126816 restraints weight = 7488.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6771  Z= 0.114
  Angle     :  0.645  14.540   9202  Z= 0.306
  Chirality :  0.046   0.511    970
  Planarity :  0.005   0.063   1169
  Dihedral  : 10.958 106.722   1017
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.96 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.01 (0.31), residues: 787
  helix:  0.28 (0.29), residues: 361
  sheet: -0.06 (0.77), residues: 47
  loop : -1.72 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 167 
 HIS   0.003   0.001   HIS A 240 
 PHE   0.023   0.001   PHE A 511 
 TYR   0.020   0.001   TYR A 198 
 ARG   0.004   0.000   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01006 (    6)
  link_NAG-ASN         : angle       4.35610 (   18)
  hydrogen bonds       : bond        0.03489 (  240)
  hydrogen bonds       : angle       4.45457 (  672)
  SS BOND              : bond        0.00446 (    5)
  SS BOND              : angle       1.87623 (   10)
  covalent geometry    : bond        0.00255 ( 6759)
  covalent geometry    : angle       0.61353 ( 9174)
  Misc. bond           : bond        0.00034 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5983 (tmm) cc_final: 0.5704 (tmm)
REVERT: A  151 MET cc_start: 0.7153 (tpt) cc_final: 0.6558 (tpt)
REVERT: A  164 TRP cc_start: 0.5534 (m100) cc_final: 0.5097 (m100)
REVERT: A  301 TRP cc_start: 0.6593 (t60) cc_final: 0.6347 (t60)
REVERT: A  340 LYS cc_start: 0.8460 (mmtm) cc_final: 0.7943 (mptt)
REVERT: A  362 LYS cc_start: 0.6686 (tttm) cc_final: 0.6462 (ttpp)
REVERT: A  507 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6467 (mm-30)
REVERT: B  346 ARG cc_start: 0.6957 (tpt-90) cc_final: 0.6738 (mtp85)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2201
  time to fit residues: 41.3128
Evaluate side-chains
  111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0040
   chunk 36 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.9596

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

Flipped N/Q/H residues before XYZ refinement:
A 299 GLN
A 373 HIS
A 598 ASN
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.121956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.118592 restraints weight = 10225.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.119177 restraints weight = 7678.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.119281 restraints weight = 5978.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6771  Z= 0.152
  Angle     :  0.653  14.476   9202  Z= 0.314
  Chirality :  0.047   0.536    970
  Planarity :  0.005   0.058   1169
  Dihedral  :  7.327  60.163   1017
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.97 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.74 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.12 (0.31), residues: 787
  helix:  0.29 (0.29), residues: 361
  sheet:  0.04 (0.82), residues: 47
  loop : -1.92 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 167 
 HIS   0.006   0.001   HIS A 373 
 PHE   0.012   0.001   PHE A 437 
 TYR   0.011   0.001   TYR A 216 
 ARG   0.003   0.000   ARG A 160 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01047 (    6)
  link_NAG-ASN         : angle       4.59261 (   18)
  hydrogen bonds       : bond        0.03857 (  240)
  hydrogen bonds       : angle       4.34206 (  672)
  SS BOND              : bond        0.00533 (    5)
  SS BOND              : angle       1.51197 (   10)
  covalent geometry    : bond        0.00347 ( 6759)
  covalent geometry    : angle       0.61916 ( 9174)
  Misc. bond           : bond        0.00069 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5830 (tmm) cc_final: 0.5594 (tmm)
REVERT: A  237 GLU cc_start: 0.6613 (tt0) cc_final: 0.6097 (mt-10)
REVERT: A  269 MET cc_start: 0.5722 (mmm) cc_final: 0.4720 (mmm)
REVERT: A  340 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8192 (mptt)
REVERT: A  454 MET cc_start: 0.7124 (tpt) cc_final: 0.6622 (tpt)
REVERT: A  479 MET cc_start: 0.7212 (ppp) cc_final: 0.6662 (ppp)
REVERT: A  488 GLU cc_start: 0.5633 (pp20) cc_final: 0.5421 (pp20)
REVERT: B  366 SER cc_start: 0.6876 (m) cc_final: 0.6644 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2341
  time to fit residues: 40.4147
Evaluate side-chains
  112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 69 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0670
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 373 HIS
B 409 GLN
B 422 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.122848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.122794 restraints weight = 10190.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.122794 restraints weight = 9007.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.122794 restraints weight = 8142.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6771  Z= 0.117
  Angle     :  0.598  13.714   9202  Z= 0.290
  Chirality :  0.045   0.517    970
  Planarity :  0.004   0.052   1169
  Dihedral  :  6.372  53.291   1017
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.08 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.59 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.31), residues: 787
  helix:  0.14 (0.28), residues: 374
  sheet: -0.02 (0.81), residues: 47
  loop : -1.83 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 472 
 HIS   0.007   0.001   HIS A 377 
 PHE   0.013   0.001   PHE A 591 
 TYR   0.009   0.001   TYR A 216 
 ARG   0.002   0.000   ARG A 459 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00940 (    6)
  link_NAG-ASN         : angle       4.18287 (   18)
  hydrogen bonds       : bond        0.03380 (  240)
  hydrogen bonds       : angle       4.13584 (  672)
  SS BOND              : bond        0.00451 (    5)
  SS BOND              : angle       1.21290 (   10)
  covalent geometry    : bond        0.00269 ( 6759)
  covalent geometry    : angle       0.56789 ( 9174)
  Misc. bond           : bond        0.00031 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5887 (tmm) cc_final: 0.5628 (tmm)
REVERT: A  133 LEU cc_start: 0.8015 (tp) cc_final: 0.7589 (tt)
REVERT: A  164 TRP cc_start: 0.5769 (m100) cc_final: 0.5563 (m100)
REVERT: A  340 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8264 (mmtm)
REVERT: A  454 MET cc_start: 0.7160 (tpt) cc_final: 0.6730 (tpp)
REVERT: A  479 MET cc_start: 0.7189 (ppp) cc_final: 0.6505 (ppp)
REVERT: A  507 GLU cc_start: 0.6478 (mm-30) cc_final: 0.6180 (mm-30)
REVERT: B  428 ASP cc_start: 0.8294 (p0) cc_final: 0.7975 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1993
  time to fit residues: 33.7122
Evaluate side-chains
  112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0870
   chunk 39 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
A 373 HIS
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.123225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.116333 restraints weight = 101068.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.117819 restraints weight = 74519.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.118536 restraints weight = 55450.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6771  Z= 0.122
  Angle     :  0.603  13.243   9202  Z= 0.293
  Chirality :  0.045   0.517    970
  Planarity :  0.004   0.049   1169
  Dihedral  :  6.131  48.939   1017
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.46 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.08 (0.31), residues: 787
  helix:  0.19 (0.28), residues: 373
  sheet:  0.01 (0.82), residues: 45
  loop : -1.78 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 472 
 HIS   0.004   0.001   HIS A 377 
 PHE   0.019   0.001   PHE A 511 
 TYR   0.009   0.001   TYR A 216 
 ARG   0.003   0.000   ARG A  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00920 (    6)
  link_NAG-ASN         : angle       4.07113 (   18)
  hydrogen bonds       : bond        0.03525 (  240)
  hydrogen bonds       : angle       4.10288 (  672)
  SS BOND              : bond        0.00412 (    5)
  SS BOND              : angle       1.07888 (   10)
  covalent geometry    : bond        0.00279 ( 6759)
  covalent geometry    : angle       0.57562 ( 9174)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6149 (tmm) cc_final: 0.5848 (tmm)
REVERT: A  164 TRP cc_start: 0.5694 (m100) cc_final: 0.5434 (m100)
REVERT: A  340 LYS cc_start: 0.8725 (mmtm) cc_final: 0.8292 (mmtm)
REVERT: A  349 ASP cc_start: 0.7161 (t0) cc_final: 0.6769 (t0)
REVERT: B  428 ASP cc_start: 0.8412 (p0) cc_final: 0.8121 (p0)
REVERT: B  481 LYS cc_start: 0.7161 (mmtp) cc_final: 0.6886 (tmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1906
  time to fit residues: 32.1148
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0970
   chunk 74 optimal weight:    0.2980
   chunk 52 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 55 optimal weight:    0.1980
   chunk 46 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.3378

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 HIS
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.124517 restraints weight = 10169.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.122205 restraints weight = 15982.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.122442 restraints weight = 13379.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6771  Z= 0.102
  Angle     :  0.591  11.937   9202  Z= 0.283
  Chirality :  0.044   0.467    970
  Planarity :  0.004   0.038   1169
  Dihedral  :  5.658  41.771   1017
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.96 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.90 (0.31), residues: 787
  helix:  0.36 (0.29), residues: 364
  sheet:  0.54 (0.81), residues: 44
  loop : -1.72 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 605 
 HIS   0.004   0.001   HIS A 377 
 PHE   0.011   0.001   PHE A 591 
 TYR   0.011   0.001   TYR A 254 
 ARG   0.004   0.000   ARG A  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00790 (    6)
  link_NAG-ASN         : angle       3.62475 (   18)
  hydrogen bonds       : bond        0.03166 (  240)
  hydrogen bonds       : angle       3.96860 (  672)
  SS BOND              : bond        0.00377 (    5)
  SS BOND              : angle       1.69448 (   10)
  covalent geometry    : bond        0.00230 ( 6759)
  covalent geometry    : angle       0.56670 ( 9174)
  Misc. bond           : bond        0.00015 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6022 (tmm) cc_final: 0.5720 (tmm)
REVERT: A  269 MET cc_start: 0.5406 (mmm) cc_final: 0.4247 (mmm)
REVERT: A  340 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8221 (mmtm)
REVERT: A  349 ASP cc_start: 0.6827 (t0) cc_final: 0.6616 (t0)
REVERT: B  428 ASP cc_start: 0.8424 (p0) cc_final: 0.8132 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1910
  time to fit residues: 31.1045
Evaluate side-chains
  105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0870
   chunk 77 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0270
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5216

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

Flipped N/Q/H residues before XYZ refinement:
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.124574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.122416 restraints weight = 9956.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.121440 restraints weight = 9808.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.121750 restraints weight = 7141.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6771  Z= 0.112
  Angle     :  0.592  11.468   9202  Z= 0.290
  Chirality :  0.045   0.462    970
  Planarity :  0.004   0.038   1169
  Dihedral  :  5.533  37.544   1017
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.96 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.92 (0.31), residues: 787
  helix:  0.41 (0.29), residues: 359
  sheet:  0.15 (0.81), residues: 47
  loop : -1.75 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 377 
 PHE   0.019   0.001   PHE A 511 
 TYR   0.011   0.001   TYR A 254 
 ARG   0.001   0.000   ARG B 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00800 (    6)
  link_NAG-ASN         : angle       3.57204 (   18)
  hydrogen bonds       : bond        0.03259 (  240)
  hydrogen bonds       : angle       3.98813 (  672)
  SS BOND              : bond        0.00579 (    5)
  SS BOND              : angle       1.82408 (   10)
  covalent geometry    : bond        0.00252 ( 6759)
  covalent geometry    : angle       0.56829 ( 9174)
  Misc. bond           : bond        0.00001 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6164 (tmm) cc_final: 0.5930 (tmm)
REVERT: A  269 MET cc_start: 0.5841 (mmm) cc_final: 0.4527 (mmm)
REVERT: A  340 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8179 (mmtm)
REVERT: A  349 ASP cc_start: 0.6861 (t0) cc_final: 0.6656 (t0)
REVERT: B  428 ASP cc_start: 0.8454 (p0) cc_final: 0.8205 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1911
  time to fit residues: 30.6255
Evaluate side-chains
  107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    0.0060
   chunk 41 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.123149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.120637 restraints weight = 10125.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.120709 restraints weight = 8686.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.120885 restraints weight = 7811.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6771  Z= 0.117
  Angle     :  0.592  11.466   9202  Z= 0.287
  Chirality :  0.045   0.469    970
  Planarity :  0.004   0.036   1169
  Dihedral  :  5.535  36.856   1017
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.08 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.90 (0.31), residues: 787
  helix:  0.42 (0.29), residues: 365
  sheet:  0.02 (0.81), residues: 48
  loop : -1.74 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 605 
 HIS   0.006   0.001   HIS A 377 
 PHE   0.011   0.001   PHE A 591 
 TYR   0.009   0.001   TYR A 453 
 ARG   0.001   0.000   ARG A 160 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00806 (    6)
  link_NAG-ASN         : angle       3.59257 (   18)
  hydrogen bonds       : bond        0.03365 (  240)
  hydrogen bonds       : angle       4.01919 (  672)
  SS BOND              : bond        0.00478 (    5)
  SS BOND              : angle       1.85309 (   10)
  covalent geometry    : bond        0.00265 ( 6759)
  covalent geometry    : angle       0.56796 ( 9174)
  Misc. bond           : bond        0.00004 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6078 (tmm) cc_final: 0.5785 (tmm)
REVERT: A  269 MET cc_start: 0.6043 (mmm) cc_final: 0.4690 (mmm)
REVERT: A  297 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6487 (mt-10)
REVERT: A  340 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8181 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1836
  time to fit residues: 30.7808
Evaluate side-chains
  113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0060
   chunk 68 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 38 optimal weight:    0.1980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.123474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.123015 restraints weight = 10147.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.122980 restraints weight = 12350.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.123004 restraints weight = 10049.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6862
moved from start:          0.3007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6771  Z= 0.111
  Angle     :  0.606  11.728   9202  Z= 0.292
  Chirality :  0.044   0.451    970
  Planarity :  0.004   0.044   1169
  Dihedral  :  5.449  34.855   1017
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.46 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.31), residues: 787
  helix:  0.50 (0.29), residues: 360
  sheet:  0.06 (0.83), residues: 46
  loop : -1.69 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 164 
 HIS   0.004   0.001   HIS A 377 
 PHE   0.009   0.001   PHE A 539 
 TYR   0.010   0.001   TYR B 380 
 ARG   0.002   0.000   ARG A 191 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00766 (    6)
  link_NAG-ASN         : angle       3.43695 (   18)
  hydrogen bonds       : bond        0.03239 (  240)
  hydrogen bonds       : angle       3.96325 (  672)
  SS BOND              : bond        0.00428 (    5)
  SS BOND              : angle       1.79830 (   10)
  covalent geometry    : bond        0.00253 ( 6759)
  covalent geometry    : angle       0.58433 ( 9174)
  Misc. bond           : bond        0.00006 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6059 (tmm) cc_final: 0.5813 (tmm)
REVERT: A  269 MET cc_start: 0.5841 (mmm) cc_final: 0.4510 (mmm)
REVERT: A  340 LYS cc_start: 0.8517 (mmtm) cc_final: 0.8157 (mmtm)
REVERT: A  349 ASP cc_start: 0.6571 (t0) cc_final: 0.6207 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2431
  time to fit residues: 38.8091
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 6 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 16 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.122336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.120352 restraints weight = 10279.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.120245 restraints weight = 11950.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.120301 restraints weight = 9924.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6771  Z= 0.122
  Angle     :  0.618  11.489   9202  Z= 0.299
  Chirality :  0.045   0.456    970
  Planarity :  0.004   0.042   1169
  Dihedral  :  5.485  33.855   1017
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.72 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.90 (0.31), residues: 787
  helix:  0.43 (0.29), residues: 360
  sheet: -0.25 (0.79), residues: 51
  loop : -1.69 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 605 
 HIS   0.004   0.001   HIS A 240 
 PHE   0.011   0.001   PHE A 591 
 TYR   0.009   0.001   TYR B 380 
 ARG   0.002   0.000   ARG A 191 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00785 (    6)
  link_NAG-ASN         : angle       3.48259 (   18)
  hydrogen bonds       : bond        0.03455 (  240)
  hydrogen bonds       : angle       4.02127 (  672)
  SS BOND              : bond        0.00431 (    5)
  SS BOND              : angle       1.83904 (   10)
  covalent geometry    : bond        0.00280 ( 6759)
  covalent geometry    : angle       0.59673 ( 9174)
  Misc. bond           : bond        0.00011 (    1)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.6112 (tmm) cc_final: 0.5881 (tmm)
REVERT: A  164 TRP cc_start: 0.5959 (m100) cc_final: 0.5582 (m100)
REVERT: A  340 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8142 (mmtm)
REVERT: A  349 ASP cc_start: 0.6591 (t0) cc_final: 0.6387 (t0)
REVERT: B  437 ASN cc_start: 0.8753 (t0) cc_final: 0.8539 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2054
  time to fit residues: 34.9966
Evaluate side-chains
  113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0980
   chunk 60 optimal weight:    0.9980
   chunk 14 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0670
   chunk 4 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.123286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.121254 restraints weight = 10242.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.121264 restraints weight = 9150.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.121264 restraints weight = 8960.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6885
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6771  Z= 0.112
  Angle     :  0.607  11.289   9202  Z= 0.297
  Chirality :  0.044   0.431    970
  Planarity :  0.004   0.048   1169
  Dihedral  :  5.307  31.341   1017
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.59 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.31), residues: 787
  helix:  0.47 (0.29), residues: 362
  sheet: -0.19 (0.77), residues: 53
  loop : -1.69 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A 377 
 PHE   0.011   0.001   PHE A 399 
 TYR   0.009   0.001   TYR B 380 
 ARG   0.004   0.000   ARG A 356 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00728 (    6)
  link_NAG-ASN         : angle       3.28247 (   18)
  hydrogen bonds       : bond        0.03172 (  240)
  hydrogen bonds       : angle       3.92205 (  672)
  SS BOND              : bond        0.00442 (    5)
  SS BOND              : angle       1.61343 (   10)
  covalent geometry    : bond        0.00255 ( 6759)
  covalent geometry    : angle       0.58795 ( 9174)
  Misc. bond           : bond        0.00005 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2402.24 seconds
wall clock time: 42 minutes 48.96 seconds (2568.96 seconds total)