Starting phenix.real_space_refine
on Wed Sep 17 07:13:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y32_38866/09_2025/8y32_38866.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y32_38866/09_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_38866/09_2025/8y32_38866.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y32_38866/09_2025/8y32_38866.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y32_38866/09_2025/8y32_38866.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y32_38866/09_2025/8y32_38866.cif"
  }
  resolution = 4.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.89, per 1000 atoms: 0.29
  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: 0.54
  Conformation dependent library (CDL) restraints added in 416.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.27
  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: 0.96

  Time building geometry restraints manager: 0.71 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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.400
  Find NCS groups from input model:        0.020
  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:2.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.980
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (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
 ARG   0.003   0.000   ARG A  66 
 TYR   0.009   0.001   TYR A 214 
 PHE   0.012   0.001   PHE B 429 
 TRP   0.024   0.001   TRP A 202 
 HIS   0.004   0.001   HIS A 102 

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

*********************** 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  : 0.250 
Fit side-chains
REVERT: A  186 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7150 (tt0)
REVERT: A  254 TYR cc_start: 0.7481 (m-80) cc_final: 0.7184 (m-10)
REVERT: A  381 ASP cc_start: 0.6680 (t0) cc_final: 0.6170 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 117
  average time/residue: 0.0854
  time to fit residues: 13.5088
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  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 422 ASN
B 439 ASN
B 474 GLN
B 477 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.124595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.121826 restraints weight = 10009.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.122071 restraints weight = 8064.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.122073 restraints weight = 6981.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122195 restraints weight = 6604.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.122247 restraints weight = 6314.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6771  Z= 0.150
  Angle     :  0.688  15.706   9202  Z= 0.330
  Chirality :  0.048   0.540    970
  Planarity :  0.005   0.064   1169
  Dihedral  : 10.934 104.101   1017
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.84 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.03 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.31), residues: 787
  helix:  0.14 (0.29), residues: 360
  sheet: -0.11 (0.78), residues: 47
  loop : -1.81 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 176 
 TYR   0.015   0.001   TYR A 198 
 PHE   0.021   0.002   PHE A 511 
 TRP   0.021   0.002   TRP A 167 
 HIS   0.005   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6759)
  covalent geometry    : angle       0.65293 ( 9174)
  SS BOND              : bond        0.00590 (    5)
  SS BOND              : angle       1.98549 (   10)
  hydrogen bonds       : bond        0.04103 (  240)
  hydrogen bonds       : angle       4.61915 (  672)
  Misc. bond           : bond        0.00028 (    1)
  link_NAG-ASN         : bond        0.01142 (    6)
  link_NAG-ASN         : angle       4.77066 (   18)

*********************** 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
  141 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5946 (tmm) cc_final: 0.5738 (tmm)
REVERT: A  151 MET cc_start: 0.7383 (tpt) cc_final: 0.6993 (tpp)
REVERT: A  164 TRP cc_start: 0.5590 (m100) cc_final: 0.5378 (m100)
REVERT: A  237 GLU cc_start: 0.6611 (tt0) cc_final: 0.6080 (mt-10)
REVERT: A  301 TRP cc_start: 0.6780 (t60) cc_final: 0.6260 (t60)
REVERT: A  340 LYS cc_start: 0.8569 (mmtm) cc_final: 0.7989 (mptt)
REVERT: A  507 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6486 (mm-30)
REVERT: B  346 ARG cc_start: 0.6989 (tpt-90) cc_final: 0.6558 (mtp85)
REVERT: B  378 LYS cc_start: 0.8160 (pttt) cc_final: 0.7851 (ptmm)
  outliers start: 1
  outliers final: 1
  residues processed: 141
  average time/residue: 0.0974
  time to fit residues: 17.8661
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 21 optimal weight:    0.0980
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.123846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.120767 restraints weight = 10081.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.121310 restraints weight = 7355.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.121399 restraints weight = 5524.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.121751 restraints weight = 4862.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.121755 restraints weight = 4214.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6771  Z= 0.130
  Angle     :  0.633  14.725   9202  Z= 0.305
  Chirality :  0.046   0.529    970
  Planarity :  0.005   0.054   1169
  Dihedral  :  7.124  60.899   1017
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.21 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.30), residues: 787
  helix:  0.21 (0.29), residues: 358
  sheet: -0.06 (0.79), residues: 47
  loop : -1.82 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 339 
 TYR   0.010   0.001   TYR A 216 
 PHE   0.033   0.001   PHE A 437 
 TRP   0.018   0.002   TRP A 472 
 HIS   0.004   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6759)
  covalent geometry    : angle       0.59914 ( 9174)
  SS BOND              : bond        0.00532 (    5)
  SS BOND              : angle       1.48688 (   10)
  hydrogen bonds       : bond        0.03596 (  240)
  hydrogen bonds       : angle       4.24693 (  672)
  Misc. bond           : bond        0.00125 (    1)
  link_NAG-ASN         : bond        0.00909 (    6)
  link_NAG-ASN         : angle       4.51733 (   18)

*********************** 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
  132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5825 (tmm) cc_final: 0.5557 (tmm)
REVERT: A  151 MET cc_start: 0.7225 (tpt) cc_final: 0.6879 (tpt)
REVERT: A  164 TRP cc_start: 0.5676 (m100) cc_final: 0.5161 (m100)
REVERT: A  237 GLU cc_start: 0.6560 (tt0) cc_final: 0.6124 (mt-10)
REVERT: A  269 MET cc_start: 0.5334 (mmm) cc_final: 0.4457 (mmm)
REVERT: A  340 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8218 (mptt)
REVERT: A  454 MET cc_start: 0.7104 (tpt) cc_final: 0.6753 (tpp)
REVERT: A  479 MET cc_start: 0.7071 (ppp) cc_final: 0.6632 (ppp)
REVERT: B  437 ASN cc_start: 0.8796 (t0) cc_final: 0.8500 (t0)
REVERT: B  444 LYS cc_start: 0.7728 (ptpt) cc_final: 0.7508 (ptpt)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0992
  time to fit residues: 16.9906
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  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0670
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 379 GLN
B 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.122059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.120455 restraints weight = 10216.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.120344 restraints weight = 13089.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.120379 restraints weight = 10891.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.120388 restraints weight = 9462.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.120409 restraints weight = 9341.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6771  Z= 0.118
  Angle     :  0.596  13.827   9202  Z= 0.289
  Chirality :  0.045   0.513    970
  Planarity :  0.004   0.050   1169
  Dihedral  :  6.302  51.929   1017
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.97 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.31), residues: 787
  helix:  0.29 (0.29), residues: 359
  sheet:  0.07 (0.81), residues: 45
  loop : -1.69 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  66 
 TYR   0.010   0.001   TYR A 216 
 PHE   0.021   0.001   PHE A 437 
 TRP   0.017   0.001   TRP A 605 
 HIS   0.009   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6759)
  covalent geometry    : angle       0.56543 ( 9174)
  SS BOND              : bond        0.00409 (    5)
  SS BOND              : angle       1.22538 (   10)
  hydrogen bonds       : bond        0.03415 (  240)
  hydrogen bonds       : angle       4.11893 (  672)
  Misc. bond           : bond        0.00016 (    1)
  link_NAG-ASN         : bond        0.00973 (    6)
  link_NAG-ASN         : angle       4.22946 (   18)

*********************** 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
  125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5894 (tmm) cc_final: 0.5603 (tmm)
REVERT: A  133 LEU cc_start: 0.8043 (tp) cc_final: 0.7699 (tt)
REVERT: A  164 TRP cc_start: 0.5768 (m100) cc_final: 0.5419 (m100)
REVERT: A  340 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8253 (mmtm)
REVERT: A  454 MET cc_start: 0.7045 (tpt) cc_final: 0.6648 (tpp)
REVERT: A  479 MET cc_start: 0.7160 (ppp) cc_final: 0.6419 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0904
  time to fit residues: 14.9213
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  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.115083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.112324 restraints weight = 10497.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.112637 restraints weight = 8032.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.112830 restraints weight = 6991.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.112908 restraints weight = 6414.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.112970 restraints weight = 5493.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.095   6771  Z= 0.260
  Angle     :  0.783  15.799   9202  Z= 0.390
  Chirality :  0.053   0.604    970
  Planarity :  0.005   0.053   1169
  Dihedral  :  7.579  63.640   1017
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.99 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.30), residues: 787
  helix: -0.34 (0.27), residues: 370
  sheet: -0.18 (0.81), residues: 45
  loop : -2.15 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 558 
 TYR   0.015   0.002   TYR B 453 
 PHE   0.020   0.002   PHE A 399 
 TRP   0.034   0.003   TRP A 605 
 HIS   0.011   0.002   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 6759)
  covalent geometry    : angle       0.74689 ( 9174)
  SS BOND              : bond        0.00418 (    5)
  SS BOND              : angle       1.99811 (   10)
  hydrogen bonds       : bond        0.05370 (  240)
  hydrogen bonds       : angle       4.65705 (  672)
  Misc. bond           : bond        0.00029 (    1)
  link_NAG-ASN         : bond        0.01345 (    6)
  link_NAG-ASN         : angle       5.19672 (   18)

*********************** 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
  140 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5718 (tmm) cc_final: 0.5503 (tmm)
REVERT: A  237 GLU cc_start: 0.6758 (tt0) cc_final: 0.6343 (mt-10)
REVERT: A  269 MET cc_start: 0.5889 (mmm) cc_final: 0.5338 (mmm)
REVERT: A  340 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8308 (mmtm)
REVERT: A  409 LEU cc_start: 0.8545 (tt) cc_final: 0.8211 (tp)
REVERT: A  428 HIS cc_start: 0.5823 (p-80) cc_final: 0.5613 (p-80)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0839
  time to fit residues: 15.7281
Evaluate side-chains
  120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 585 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.119358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.117310 restraints weight = 10382.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.117192 restraints weight = 13335.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.117556 restraints weight = 9862.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.117528 restraints weight = 6865.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.117774 restraints weight = 5358.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6771  Z= 0.135
  Angle     :  0.654  14.862   9202  Z= 0.319
  Chirality :  0.047   0.553    970
  Planarity :  0.004   0.042   1169
  Dihedral  :  6.775  57.146   1017
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.84 %
    Favored  : 93.90 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.30), residues: 787
  helix: -0.24 (0.28), residues: 381
  sheet:  0.03 (0.81), residues: 44
  loop : -1.94 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.011   0.001   TYR B 380 
 PHE   0.021   0.002   PHE A 511 
 TRP   0.022   0.002   TRP A 167 
 HIS   0.004   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6759)
  covalent geometry    : angle       0.62184 ( 9174)
  SS BOND              : bond        0.00514 (    5)
  SS BOND              : angle       1.56572 (   10)
  hydrogen bonds       : bond        0.03757 (  240)
  hydrogen bonds       : angle       4.27374 (  672)
  Misc. bond           : bond        0.00013 (    1)
  link_NAG-ASN         : bond        0.00997 (    6)
  link_NAG-ASN         : angle       4.49672 (   18)

*********************** 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
  131 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5672 (tmm) cc_final: 0.5365 (tmm)
REVERT: A  148 ASP cc_start: 0.7351 (t0) cc_final: 0.5212 (t0)
REVERT: A  164 TRP cc_start: 0.6131 (m100) cc_final: 0.5662 (m100)
REVERT: A  304 GLU cc_start: 0.6898 (pm20) cc_final: 0.6693 (pm20)
REVERT: A  340 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8299 (mmtm)
REVERT: A  409 LEU cc_start: 0.8569 (tt) cc_final: 0.8319 (tp)
REVERT: A  428 HIS cc_start: 0.5700 (p-80) cc_final: 0.5475 (p-80)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0910
  time to fit residues: 15.7921
Evaluate side-chains
  117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0870
   chunk 47 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 400 HIS
B 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.121393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.120956 restraints weight = 10087.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.120905 restraints weight = 11839.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.120881 restraints weight = 10478.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120786 restraints weight = 9120.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.120726 restraints weight = 10165.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6771  Z= 0.123
  Angle     :  0.643  13.988   9202  Z= 0.313
  Chirality :  0.046   0.526    970
  Planarity :  0.004   0.040   1169
  Dihedral  :  6.229  49.720   1017
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.59 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.31), residues: 787
  helix:  0.03 (0.29), residues: 370
  sheet:  0.27 (0.80), residues: 46
  loop : -2.00 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  66 
 TYR   0.015   0.001   TYR A 182 
 PHE   0.015   0.001   PHE A 399 
 TRP   0.018   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6759)
  covalent geometry    : angle       0.61188 ( 9174)
  SS BOND              : bond        0.00486 (    5)
  SS BOND              : angle       2.10669 (   10)
  hydrogen bonds       : bond        0.03523 (  240)
  hydrogen bonds       : angle       4.15667 (  672)
  Misc. bond           : bond        0.00008 (    1)
  link_NAG-ASN         : bond        0.00936 (    6)
  link_NAG-ASN         : angle       4.21890 (   18)

*********************** 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
  123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5747 (tmm) cc_final: 0.5489 (tmm)
REVERT: A  151 MET cc_start: 0.7640 (tpt) cc_final: 0.7321 (tpt)
REVERT: A  164 TRP cc_start: 0.5926 (m100) cc_final: 0.5333 (m100)
REVERT: A  340 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8294 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0896
  time to fit residues: 14.5959
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0040
   chunk 14 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 39 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
A 400 HIS
** B 422 ASN ** 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 = 0.3359 r_free = 0.3359 target = 0.122860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122631 restraints weight = 10132.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.122395 restraints weight = 10605.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.122125 restraints weight = 15970.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.122121 restraints weight = 15518.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.122140 restraints weight = 11409.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6771  Z= 0.110
  Angle     :  0.606  12.787   9202  Z= 0.296
  Chirality :  0.045   0.492    970
  Planarity :  0.004   0.037   1169
  Dihedral  :  5.769  42.245   1017
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.83 %
    Favored  : 94.92 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.31), residues: 787
  helix:  0.04 (0.28), residues: 375
  sheet:  0.31 (0.81), residues: 46
  loop : -1.82 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  66 
 TYR   0.009   0.001   TYR B 380 
 PHE   0.013   0.001   PHE A 437 
 TRP   0.016   0.001   TRP A 167 
 HIS   0.004   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6759)
  covalent geometry    : angle       0.57928 ( 9174)
  SS BOND              : bond        0.00410 (    5)
  SS BOND              : angle       1.88581 (   10)
  hydrogen bonds       : bond        0.03233 (  240)
  hydrogen bonds       : angle       4.03104 (  672)
  Misc. bond           : bond        0.00008 (    1)
  link_NAG-ASN         : bond        0.00851 (    6)
  link_NAG-ASN         : angle       3.86590 (   18)

*********************** 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
  122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5852 (tmm) cc_final: 0.5635 (tmm)
REVERT: A  269 MET cc_start: 0.4894 (mmm) cc_final: 0.3685 (mmm)
REVERT: A  340 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8278 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0899
  time to fit residues: 14.6469
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  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0970
   chunk 66 optimal weight:    0.0570
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.123249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.122635 restraints weight = 10178.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.122593 restraints weight = 11993.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.122620 restraints weight = 10328.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.122579 restraints weight = 8542.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.122545 restraints weight = 7014.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6875
moved from start:          0.3253

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= 0.111
  Angle     :  0.598  12.116   9202  Z= 0.293
  Chirality :  0.044   0.475    970
  Planarity :  0.004   0.036   1169
  Dihedral  :  5.558  38.496   1017
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.46 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.31), residues: 787
  helix:  0.20 (0.29), residues: 369
  sheet:  0.25 (0.79), residues: 47
  loop : -1.75 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 356 
 TYR   0.008   0.001   TYR B 380 
 PHE   0.031   0.001   PHE A 511 
 TRP   0.016   0.001   TRP A 605 
 HIS   0.004   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6759)
  covalent geometry    : angle       0.57430 ( 9174)
  SS BOND              : bond        0.00399 (    5)
  SS BOND              : angle       1.38699 (   10)
  hydrogen bonds       : bond        0.03187 (  240)
  hydrogen bonds       : angle       3.98373 (  672)
  Misc. bond           : bond        0.00014 (    1)
  link_NAG-ASN         : bond        0.00820 (    6)
  link_NAG-ASN         : angle       3.69531 (   18)

*********************** 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
  119 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5943 (tmm) cc_final: 0.5717 (tmm)
REVERT: A  269 MET cc_start: 0.4776 (mmm) cc_final: 0.3605 (mmm)
REVERT: A  340 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8249 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0773
  time to fit residues: 12.5911
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  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0770
   chunk 6 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 11 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 400 HIS
A 441 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.123309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.121539 restraints weight = 10106.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.121568 restraints weight = 8881.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.121599 restraints weight = 7886.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.121616 restraints weight = 6558.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.121619 restraints weight = 6200.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6771  Z= 0.117
  Angle     :  0.614  11.725   9202  Z= 0.302
  Chirality :  0.045   0.467    970
  Planarity :  0.004   0.038   1169
  Dihedral  :  5.539  36.556   1017
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.08 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.31), residues: 787
  helix:  0.09 (0.28), residues: 373
  sheet:  0.42 (0.80), residues: 46
  loop : -1.72 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  66 
 TYR   0.010   0.001   TYR A 453 
 PHE   0.049   0.001   PHE A 437 
 TRP   0.019   0.002   TRP A 605 
 HIS   0.004   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6759)
  covalent geometry    : angle       0.59269 ( 9174)
  SS BOND              : bond        0.00434 (    5)
  SS BOND              : angle       1.33119 (   10)
  hydrogen bonds       : bond        0.03432 (  240)
  hydrogen bonds       : angle       4.05546 (  672)
  Misc. bond           : bond        0.00017 (    1)
  link_NAG-ASN         : bond        0.00797 (    6)
  link_NAG-ASN         : angle       3.58698 (   18)

********************** 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
  117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.5939 (tmm) cc_final: 0.5693 (tmm)
REVERT: A  269 MET cc_start: 0.5245 (mmm) cc_final: 0.3484 (mmm)
REVERT: A  340 LYS cc_start: 0.8576 (mmtm) cc_final: 0.8244 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0828
  time to fit residues: 13.0579
Evaluate side-chains
  102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0050
   chunk 47 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 400 HIS
A 441 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 = 0.3360 r_free = 0.3360 target = 0.122980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.122704 restraints weight = 10234.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122674 restraints weight = 12794.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.122701 restraints weight = 10171.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122685 restraints weight = 9729.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122691 restraints weight = 7524.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6771  Z= 0.123
  Angle     :  0.612  11.618   9202  Z= 0.302
  Chirality :  0.045   0.470    970
  Planarity :  0.004   0.037   1169
  Dihedral  :  5.506  35.562   1017
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.97 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.31), residues: 787
  helix:  0.28 (0.29), residues: 361
  sheet:  0.26 (0.82), residues: 45
  loop : -1.73 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 356 
 TYR   0.009   0.001   TYR A 254 
 PHE   0.048   0.001   PHE A 437 
 TRP   0.020   0.002   TRP A 167 
 HIS   0.004   0.001   HIS A 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6759)
  covalent geometry    : angle       0.59009 ( 9174)
  SS BOND              : bond        0.00454 (    5)
  SS BOND              : angle       1.35965 (   10)
  hydrogen bonds       : bond        0.03485 (  240)
  hydrogen bonds       : angle       4.12597 (  672)
  Misc. bond           : bond        0.00023 (    1)
  link_NAG-ASN         : bond        0.00812 (    6)
  link_NAG-ASN         : angle       3.57775 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1160.82 seconds
wall clock time: 20 minutes 49.64 seconds (1249.64 seconds total)