Starting phenix.real_space_refine
on Wed Mar  4 01:50:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r10_14226/03_2026/7r10_14226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r10_14226/03_2026/7r10_14226.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r10_14226/03_2026/7r10_14226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r10_14226/03_2026/7r10_14226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r10_14226/03_2026/7r10_14226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r10_14226/03_2026/7r10_14226.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      51      5.16       5
     C    6286      2.51       5
     N    1620      2.21       5
     O    1865      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9823
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 4801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4801
          Classifications: {'peptide': 588}
          Link IDs: {'PTRANS': 25, 'TRANS': 562}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 622, 4923
          Classifications: {'peptide': 622}
          Link IDs: {'PTRANS': 32, 'TRANS': 589}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 85
          Unusual residues: {' ZN': 1, 'NAG': 6}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.88, per 1000 atoms: 0.19
  Number of scatterers: 9823
  At special positions: 0
  Unit cell: (94.864, 108.878, 164.934, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      51     16.00
     O    1865      8.00
     N    1620      7.00
     C    6286      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG D 902 " - " ASN D  53 "
      " NAG D 903 " - " ASN D  90 "
      " NAG D 904 " - " ASN D 322 "
      " NAG D 905 " - " ASN D 432 "
      " NAG D 906 " - " ASN D 546 "
      " NAG D 907 " - " ASN D 103 "
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 453.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 901 "
        pdb="ZN    ZN D 901 " - pdb=" NE2 HIS D 378 "
        pdb="ZN    ZN D 901 " - pdb=" NE2 HIS D 374 "


  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2272

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 13 sheets defined
      36.7% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.684A  pdb=" N   HIS D  34 " --> pdb=" O   ASP D  30 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   GLU D  35 " --> pdb=" O   LYS D  31 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   ASP D  38 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 81
    Processing helix  chain 'D' and resid 92 through 101
    Processing helix  chain 'D' and resid 103 through 108
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 147 through 155
    Processing helix  chain 'D' and resid 157 through 173
    Processing helix  chain 'D' and resid 176 through 194
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 218 through 224
      removed outlier: 3.668A  pdb=" N   LEU D 222 " --> pdb=" O   SER D 218 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   GLU D 224 " --> pdb=" O   GLY D 220 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 218 through 224'
    Processing helix  chain 'D' and resid 226 through 233
    Processing helix  chain 'D' and resid 233 through 249
    Processing helix  chain 'D' and resid 265 through 268
      removed outlier: 4.357A  pdb=" N   GLY D 268 " --> pdb=" O   HIS D 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 265 through 268'
    Processing helix  chain 'D' and resid 275 through 281
      removed outlier: 3.650A  pdb=" N   SER D 280 " --> pdb=" O   ASN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 301
    Processing helix  chain 'D' and resid 305 through 319
    Processing helix  chain 'D' and resid 326 through 331
      removed outlier: 3.677A  pdb=" N   SER D 331 " --> pdb=" O   PHE D 327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.799A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 413
      removed outlier: 3.771A  pdb=" N   ALA D 403 " --> pdb=" O   GLY D 399 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   SER D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.940A  pdb=" N   THR D 445 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 449 through 466
    Processing helix  chain 'D' and resid 472 through 484
    Processing helix  chain 'D' and resid 499 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
      removed outlier: 4.651A  pdb=" N   THR D 519 " --> pdb=" O   TYR D 515 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU D 520 " --> pdb=" O   TYR D 516 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 3.584A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 572
    Processing helix  chain 'D' and resid 581 through 588
    Processing helix  chain 'D' and resid 588 through 599
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.887A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 389
      removed outlier: 3.633A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.009A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263
      removed outlier: 5.661A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 30
      removed outlier: 3.939A  pdb=" N   ALA A  27 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LYS A 187 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
      removed outlier: 9.471A  pdb=" N   HIS A 207 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 9.229A  pdb=" N   LEU A 223 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55
      removed outlier: 3.847A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85
      removed outlier: 6.815A  pdb=" N   ARG A 237 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   PHE A 106 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLN A 239 " --> pdb=" O   TRP A 104 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   TRP A 104 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU A 241 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 11.012A  pdb=" N   VAL A 126 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 9.667A  pdb=" N   GLU A 169 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 11.093A  pdb=" N   ILE A 128 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
      removed outlier: 8.560A  pdb=" N   THR A 167 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL A 130 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ASN A 165 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLU A 132 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ALA A 163 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 143
      removed outlier: 5.622A  pdb=" N   LEU A 244 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313
    Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328
      removed outlier: 3.898A  pdb=" N   GLU A 324 " --> pdb=" O   CYS A 538 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ILE A 584 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB4, first strand: chain 'A' and resid 664 through 667
      removed outlier: 6.534A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)

    416 hydrogen bonds defined for protein.
    1146 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: 1.43

  Time building geometry restraints manager: 0.89 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: 3104
        1.34 -     1.46: 2360
        1.46 -     1.58: 4545
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 10083
  Sorted by residual:
  bond pdb=" N   CYS A 291 "
       pdb=" CA  CYS A 291 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.039 1.24e-02 6.50e+03 9.76e+00
  bond pdb=" N   VAL A 320 "
       pdb=" CA  VAL A 320 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.11e+00
  bond pdb=" N   ARG A 319 "
       pdb=" CA  ARG A 319 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.037 1.22e-02 6.72e+03 9.01e+00
  bond pdb=" N   LYS A 529 "
       pdb=" CA  LYS A 529 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.18e-02 7.18e+03 8.27e+00
  bond pdb=" N   ASP A 290 "
       pdb=" CA  ASP A 290 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.24e-02 6.50e+03 7.73e+00
  ... (remaining 10078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 13281
        1.31 -     2.62: 313
        2.62 -     3.93: 102
        3.93 -     5.24: 9
        5.24 -     6.54: 3
  Bond angle restraints: 13708
  Sorted by residual:
  angle pdb=" CA  CYS A 291 "
        pdb=" C   CYS A 291 "
        pdb=" O   CYS A 291 "
      ideal   model   delta    sigma   weight residual
     120.55  116.78    3.77 1.07e+00 8.73e-01 1.24e+01
  angle pdb=" CA  PHE A 318 "
        pdb=" C   PHE A 318 "
        pdb=" O   PHE A 318 "
      ideal   model   delta    sigma   weight residual
     121.55  117.93    3.62 1.06e+00 8.90e-01 1.17e+01
  angle pdb=" CA  SER A 591 "
        pdb=" C   SER A 591 "
        pdb=" O   SER A 591 "
      ideal   model   delta    sigma   weight residual
     121.55  118.37    3.18 1.06e+00 8.90e-01 9.00e+00
  angle pdb=" CA  ILE A 332 "
        pdb=" C   ILE A 332 "
        pdb=" O   ILE A 332 "
      ideal   model   delta    sigma   weight residual
     121.09  117.94    3.15 1.06e+00 8.90e-01 8.82e+00
  angle pdb=" CA  ARG A 319 "
        pdb=" C   ARG A 319 "
        pdb=" O   ARG A 319 "
      ideal   model   delta    sigma   weight residual
     121.16  117.98    3.18 1.12e+00 7.97e-01 8.06e+00
  ... (remaining 13703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 5491
       17.52 -    35.04: 437
       35.04 -    52.57: 83
       52.57 -    70.09: 19
       70.09 -    87.61: 10
  Dihedral angle restraints: 6040
    sinusoidal: 2502
      harmonic: 3538
  Sorted by residual:
  dihedral pdb=" CB  CYS A 538 "
           pdb=" SG  CYS A 538 "
           pdb=" SG  CYS A 590 "
           pdb=" CB  CYS A 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -153.14   67.14     1      1.00e+01 1.00e-02 5.87e+01
  dihedral pdb=" CB  CYS D 133 "
           pdb=" SG  CYS D 133 "
           pdb=" SG  CYS D 141 "
           pdb=" CB  CYS D 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   32.40   60.60     1      1.00e+01 1.00e-02 4.89e+01
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -38.84  -47.16     1      1.00e+01 1.00e-02 3.07e+01
  ... (remaining 6037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1147
       0.044 -    0.087: 233
       0.087 -    0.131: 103
       0.131 -    0.174: 9
       0.174 -    0.218: 2
  Chirality restraints: 1494
  Sorted by residual:
  chirality pdb=" CA  ILE A 332 "
            pdb=" N   ILE A 332 "
            pdb=" C   ILE A 332 "
            pdb=" CB  ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  VAL A 143 "
            pdb=" N   VAL A 143 "
            pdb=" C   VAL A 143 "
            pdb=" CB  VAL A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.70e-01
  chirality pdb=" CA  VAL A 320 "
            pdb=" N   VAL A 320 "
            pdb=" C   VAL A 320 "
            pdb=" CB  VAL A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.42e-01
  ... (remaining 1491 not shown)

  Planarity restraints: 1767
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D  35 "    0.016 2.00e-02 2.50e+03   3.13e-02 9.82e+00
        pdb=" C   GLU D  35 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   GLU D  35 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ALA D  36 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 478 "    0.036 5.00e-02 4.00e+02   5.45e-02 4.75e+00
        pdb=" N   PRO A 479 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 479 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 479 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 289 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.54e+00
        pdb=" C   VAL A 289 "    0.037 2.00e-02 2.50e+03
        pdb=" O   VAL A 289 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP A 290 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1764 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 176
        2.68 -     3.24: 9263
        3.24 -     3.79: 14875
        3.79 -     4.35: 19540
        4.35 -     4.90: 32679
  Nonbonded interactions: 76533
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 402 "
            pdb="ZN    ZN D 901 "
     model   vdw
     2.131 2.230
  nonbonded pdb=" O   PRO A  85 "
            pdb=" OH  TYR A 269 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ASN A  81 "
            pdb=" NE2 GLN A 239 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ASN D  53 "
            pdb=" ND2 ASN D  58 "
     model   vdw
     2.334 3.120
  ... (remaining 76528 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:             3.900
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.810
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
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      :  0.003   0.039  10105  Z= 0.187
  Angle     :  0.524   6.545  13755  Z= 0.293
  Chirality :  0.043   0.218   1494
  Planarity :  0.003   0.054   1760
  Dihedral  : 13.309  87.611   3729
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  0.19 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.25), residues: 1196
  helix:  2.25 (0.28), residues: 388
  sheet:  0.80 (0.38), residues: 182
  loop : -0.87 (0.25), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 245 
 TYR   0.012   0.001   TYR A 265 
 PHE   0.010   0.001   PHE D 512 
 TRP   0.012   0.001   TRP A 353 
 HIS   0.005   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10083)
  covalent geometry    : angle       0.51629 (13708)
  SS BOND              : bond        0.00983 (   13)
  SS BOND              : angle       1.26653 (   26)
  hydrogen bonds       : bond        0.12487 (  416)
  hydrogen bonds       : angle       5.13874 ( 1146)
  metal coordination   : bond        0.00121 (    2)
  link_NAG-ASN         : bond        0.00365 (    7)
  link_NAG-ASN         : angle       1.91630 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  190 MET cc_start: 0.9308 (ttp) cc_final: 0.9051 (tmm)
REVERT: D  270 MET cc_start: 0.8684 (tpp) cc_final: 0.8242 (tpp)
REVERT: A  177 MET cc_start: 0.4589 (ttm) cc_final: 0.4306 (mtm)
  outliers start: 5
  outliers final: 3
  residues processed: 70
  average time/residue: 0.1058
  time to fit residues: 10.6755
Evaluate side-chains
  40 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  319 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0570
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0870
   chunk 117 optimal weight:    7.9990
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
D 101 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.076324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.049798 restraints weight = 45346.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.049218 restraints weight = 28225.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.049446 restraints weight = 24389.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.049627 restraints weight = 21680.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.049731 restraints weight = 19768.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10105  Z= 0.103
  Angle     :  0.515  10.449  13755  Z= 0.259
  Chirality :  0.042   0.171   1494
  Planarity :  0.004   0.065   1760
  Dihedral  :  6.155  59.757   1463
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  4.21 %
    Favored  : 94.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.25), residues: 1196
  helix:  2.17 (0.27), residues: 385
  sheet:  0.93 (0.39), residues: 161
  loop : -0.89 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 646 
 TYR   0.011   0.001   TYR A 612 
 PHE   0.011   0.001   PHE D 230 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (10083)
  covalent geometry    : angle       0.50871 (13708)
  SS BOND              : bond        0.00176 (   13)
  SS BOND              : angle       0.52465 (   26)
  hydrogen bonds       : bond        0.03696 (  416)
  hydrogen bonds       : angle       4.48369 ( 1146)
  metal coordination   : bond        0.00070 (    2)
  link_NAG-ASN         : bond        0.00407 (    7)
  link_NAG-ASN         : angle       2.03370 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.8840 (tpp) cc_final: 0.8567 (tpt)
REVERT: D  190 MET cc_start: 0.9377 (ttp) cc_final: 0.8964 (tmm)
REVERT: D  270 MET cc_start: 0.8505 (tpp) cc_final: 0.8033 (tpp)
REVERT: D  303 ASP cc_start: 0.6856 (p0) cc_final: 0.6635 (p0)
REVERT: D  360 MET cc_start: 0.8360 (mtm) cc_final: 0.8107 (ttp)
REVERT: A  258 TRP cc_start: 0.5130 (p-90) cc_final: 0.4878 (p-90)
REVERT: A  266 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.8347 (m-80)
  outliers start: 9
  outliers final: 4
  residues processed: 47
  average time/residue: 0.1013
  time to fit residues: 7.0883
Evaluate side-chains
  40 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  646 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 36 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 32 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 115 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 146 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.075754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.049139 restraints weight = 45666.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.048597 restraints weight = 29245.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.048680 restraints weight = 23812.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.048906 restraints weight = 22592.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.048951 restraints weight = 19908.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10105  Z= 0.115
  Angle     :  0.493   7.363  13755  Z= 0.249
  Chirality :  0.041   0.175   1494
  Planarity :  0.003   0.049   1760
  Dihedral  :  5.448  55.229   1458
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  6.18 %
    Favored  : 92.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.25), residues: 1196
  helix:  2.09 (0.27), residues: 385
  sheet:  0.92 (0.39), residues: 159
  loop : -0.84 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 646 
 TYR   0.014   0.001   TYR A 612 
 PHE   0.010   0.001   PHE D 230 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10083)
  covalent geometry    : angle       0.48550 (13708)
  SS BOND              : bond        0.00162 (   13)
  SS BOND              : angle       0.50182 (   26)
  hydrogen bonds       : bond        0.03560 (  416)
  hydrogen bonds       : angle       4.39353 ( 1146)
  metal coordination   : bond        0.00081 (    2)
  link_NAG-ASN         : bond        0.00296 (    7)
  link_NAG-ASN         : angle       2.18207 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.8877 (tpp) cc_final: 0.8510 (tpt)
REVERT: D  190 MET cc_start: 0.9385 (ttp) cc_final: 0.8974 (tmm)
REVERT: D  249 MET cc_start: 0.8156 (mmt) cc_final: 0.7945 (mmt)
REVERT: D  270 MET cc_start: 0.8506 (tpp) cc_final: 0.8012 (tpp)
REVERT: D  303 ASP cc_start: 0.6934 (p0) cc_final: 0.6647 (p0)
REVERT: D  360 MET cc_start: 0.8423 (mtm) cc_final: 0.8217 (ttp)
REVERT: A  258 TRP cc_start: 0.5170 (p-90) cc_final: 0.4821 (p-90)
REVERT: A  266 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.8539 (m-80)
  outliers start: 9
  outliers final: 5
  residues processed: 43
  average time/residue: 0.0897
  time to fit residues: 5.9141
Evaluate side-chains
  39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 53 optimal weight:    0.0870
   chunk 111 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   overall best weight:    0.9760

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.075346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.048801 restraints weight = 46084.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.048188 restraints weight = 31035.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.048249 restraints weight = 24356.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.048446 restraints weight = 23076.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.048520 restraints weight = 21339.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10105  Z= 0.136
  Angle     :  0.499   7.842  13755  Z= 0.254
  Chirality :  0.041   0.184   1494
  Planarity :  0.003   0.034   1760
  Dihedral  :  5.214  56.108   1458
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.30 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.25), residues: 1196
  helix:  2.04 (0.27), residues: 386
  sheet:  1.09 (0.40), residues: 151
  loop : -0.84 (0.24), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 646 
 TYR   0.015   0.001   TYR A 612 
 PHE   0.010   0.001   PHE D 369 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10083)
  covalent geometry    : angle       0.49095 (13708)
  SS BOND              : bond        0.00166 (   13)
  SS BOND              : angle       0.54663 (   26)
  hydrogen bonds       : bond        0.03562 (  416)
  hydrogen bonds       : angle       4.38691 ( 1146)
  metal coordination   : bond        0.00150 (    2)
  link_NAG-ASN         : bond        0.00282 (    7)
  link_NAG-ASN         : angle       2.25066 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.8940 (tpp) cc_final: 0.8568 (tpt)
REVERT: D  190 MET cc_start: 0.9390 (ttp) cc_final: 0.8992 (tmm)
REVERT: D  248 LEU cc_start: 0.9265 (tp) cc_final: 0.9033 (tp)
REVERT: D  270 MET cc_start: 0.8507 (tpp) cc_final: 0.8016 (tpp)
REVERT: D  303 ASP cc_start: 0.7179 (p0) cc_final: 0.6889 (p0)
REVERT: D  332 MET cc_start: 0.8177 (ppp) cc_final: 0.7891 (tmm)
REVERT: D  360 MET cc_start: 0.8475 (mtm) cc_final: 0.8183 (ttp)
REVERT: A  177 MET cc_start: 0.1420 (mtp) cc_final: 0.1127 (mtp)
REVERT: A  266 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.8521 (m-80)
  outliers start: 11
  outliers final: 5
  residues processed: 45
  average time/residue: 0.1035
  time to fit residues: 7.0249
Evaluate side-chains
  37 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 105 optimal weight:    0.0170
   chunk 61 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 119 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0470
   overall best weight:    0.5318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.075817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.049304 restraints weight = 45401.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.048773 restraints weight = 30573.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.048852 restraints weight = 23615.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.049053 restraints weight = 22406.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.049132 restraints weight = 20745.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10105  Z= 0.097
  Angle     :  0.479   7.878  13755  Z= 0.242
  Chirality :  0.041   0.184   1494
  Planarity :  0.003   0.034   1760
  Dihedral  :  5.009  55.363   1458
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.71 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.25), residues: 1196
  helix:  2.12 (0.27), residues: 386
  sheet:  1.09 (0.40), residues: 154
  loop : -0.80 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 646 
 TYR   0.016   0.001   TYR A 612 
 PHE   0.008   0.001   PHE D 369 
 TRP   0.013   0.001   TRP A 258 
 HIS   0.002   0.000   HIS D 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (10083)
  covalent geometry    : angle       0.47171 (13708)
  SS BOND              : bond        0.00129 (   13)
  SS BOND              : angle       0.43966 (   26)
  hydrogen bonds       : bond        0.03224 (  416)
  hydrogen bonds       : angle       4.25295 ( 1146)
  metal coordination   : bond        0.00079 (    2)
  link_NAG-ASN         : bond        0.00313 (    7)
  link_NAG-ASN         : angle       2.25626 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   97 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9322 (mm)
REVERT: D  152 MET cc_start: 0.8939 (tpp) cc_final: 0.8542 (tpt)
REVERT: D  190 MET cc_start: 0.9389 (ttp) cc_final: 0.9129 (tmm)
REVERT: D  270 MET cc_start: 0.8446 (tpp) cc_final: 0.7964 (tpp)
REVERT: D  303 ASP cc_start: 0.7270 (p0) cc_final: 0.6986 (p0)
REVERT: D  332 MET cc_start: 0.8101 (ppp) cc_final: 0.7874 (tmm)
REVERT: D  360 MET cc_start: 0.8464 (mtm) cc_final: 0.8173 (ttp)
REVERT: A  177 MET cc_start: 0.1635 (mtp) cc_final: 0.1310 (mtp)
REVERT: A  266 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8453 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 40
  average time/residue: 0.0775
  time to fit residues: 5.0998
Evaluate side-chains
  39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 119 optimal weight:    0.0570
   chunk 103 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0570
   chunk 109 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 101 optimal weight:    0.8980
   chunk 105 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.4616

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.075845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.046793 restraints weight = 45450.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.048742 restraints weight = 29210.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.048668 restraints weight = 17292.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.048904 restraints weight = 18364.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.048985 restraints weight = 15678.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10105  Z= 0.089
  Angle     :  0.468   9.103  13755  Z= 0.235
  Chirality :  0.040   0.174   1494
  Planarity :  0.003   0.032   1760
  Dihedral  :  4.827  54.789   1458
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  8.80 %
    Favored  : 90.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.25), residues: 1196
  helix:  2.15 (0.28), residues: 387
  sheet:  1.14 (0.40), residues: 154
  loop : -0.78 (0.24), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 646 
 TYR   0.015   0.001   TYR A 612 
 PHE   0.008   0.001   PHE D 369 
 TRP   0.010   0.001   TRP A 258 
 HIS   0.002   0.000   HIS D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 (10083)
  covalent geometry    : angle       0.46063 (13708)
  SS BOND              : bond        0.00106 (   13)
  SS BOND              : angle       0.41596 (   26)
  hydrogen bonds       : bond        0.03039 (  416)
  hydrogen bonds       : angle       4.14904 ( 1146)
  metal coordination   : bond        0.00075 (    2)
  link_NAG-ASN         : bond        0.00306 (    7)
  link_NAG-ASN         : angle       2.22913 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   97 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9309 (mm)
REVERT: D  152 MET cc_start: 0.9007 (tpp) cc_final: 0.8619 (tpt)
REVERT: D  190 MET cc_start: 0.9348 (ttp) cc_final: 0.9094 (tmm)
REVERT: D  270 MET cc_start: 0.8480 (tpp) cc_final: 0.7954 (tpp)
REVERT: D  360 MET cc_start: 0.8343 (mtm) cc_final: 0.8035 (ttp)
REVERT: D  375 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8280 (mp0)
REVERT: D  474 MET cc_start: 0.8642 (mmp) cc_final: 0.8396 (mmm)
REVERT: A  177 MET cc_start: 0.2343 (mtp) cc_final: 0.1947 (mtp)
REVERT: A  266 TYR cc_start: 0.9389 (OUTLIER) cc_final: 0.8628 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 41
  average time/residue: 0.0884
  time to fit residues: 5.7952
Evaluate side-chains
  41 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  297 MET
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  478 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0770
   chunk 28 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 82 optimal weight:   10.0000
   chunk 87 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.7140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.075518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.048764 restraints weight = 45437.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.048361 restraints weight = 28559.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.048394 restraints weight = 23446.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.048642 restraints weight = 22364.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.048821 restraints weight = 19795.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10105  Z= 0.107
  Angle     :  0.473   9.628  13755  Z= 0.238
  Chirality :  0.040   0.173   1494
  Planarity :  0.003   0.032   1760
  Dihedral  :  4.833  55.609   1458
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  8.99 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.25), residues: 1196
  helix:  2.10 (0.27), residues: 391
  sheet:  1.13 (0.40), residues: 155
  loop : -0.77 (0.25), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 454 
 TYR   0.016   0.001   TYR D  50 
 PHE   0.009   0.001   PHE D 369 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.000   HIS D 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (10083)
  covalent geometry    : angle       0.46562 (13708)
  SS BOND              : bond        0.00131 (   13)
  SS BOND              : angle       0.45421 (   26)
  hydrogen bonds       : bond        0.03193 (  416)
  hydrogen bonds       : angle       4.15912 ( 1146)
  metal coordination   : bond        0.00091 (    2)
  link_NAG-ASN         : bond        0.00292 (    7)
  link_NAG-ASN         : angle       2.22337 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   97 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9315 (mm)
REVERT: D  152 MET cc_start: 0.9020 (tpp) cc_final: 0.8651 (tpt)
REVERT: D  190 MET cc_start: 0.9371 (ttp) cc_final: 0.9136 (tmm)
REVERT: D  248 LEU cc_start: 0.9285 (tp) cc_final: 0.9028 (tp)
REVERT: D  270 MET cc_start: 0.8471 (tpp) cc_final: 0.7991 (tpp)
REVERT: D  360 MET cc_start: 0.8363 (mtm) cc_final: 0.8020 (ttp)
REVERT: D  375 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8286 (mp0)
REVERT: D  474 MET cc_start: 0.8723 (mmp) cc_final: 0.8514 (mmm)
REVERT: A  177 MET cc_start: 0.1507 (mtp) cc_final: 0.1242 (mtp)
REVERT: A  266 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8431 (m-80)
  outliers start: 13
  outliers final: 6
  residues processed: 43
  average time/residue: 0.0867
  time to fit residues: 6.0302
Evaluate side-chains
  40 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  297 MET
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  478 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 78 optimal weight:    8.9990
   chunk 119 optimal weight:    8.9990
   chunk 16 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 18 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.9584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.075083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.046046 restraints weight = 45076.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.047943 restraints weight = 29345.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.047498 restraints weight = 17788.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.047890 restraints weight = 19194.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.047876 restraints weight = 17188.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10105  Z= 0.131
  Angle     :  0.497   9.724  13755  Z= 0.251
  Chirality :  0.041   0.175   1494
  Planarity :  0.003   0.034   1760
  Dihedral  :  4.904  56.093   1458
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.64 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.25), residues: 1196
  helix:  2.05 (0.27), residues: 391
  sheet:  1.18 (0.40), residues: 152
  loop : -0.75 (0.25), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 454 
 TYR   0.014   0.001   TYR D 207 
 PHE   0.010   0.001   PHE D 369 
 TRP   0.008   0.001   TRP A 258 
 HIS   0.003   0.000   HIS D 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10083)
  covalent geometry    : angle       0.48972 (13708)
  SS BOND              : bond        0.00150 (   13)
  SS BOND              : angle       0.50924 (   26)
  hydrogen bonds       : bond        0.03356 (  416)
  hydrogen bonds       : angle       4.26237 ( 1146)
  metal coordination   : bond        0.00151 (    2)
  link_NAG-ASN         : bond        0.00275 (    7)
  link_NAG-ASN         : angle       2.23541 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   97 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9319 (mm)
REVERT: D  152 MET cc_start: 0.9037 (tpp) cc_final: 0.8650 (tpt)
REVERT: D  190 MET cc_start: 0.9377 (ttp) cc_final: 0.9130 (tmm)
REVERT: D  270 MET cc_start: 0.8514 (tpp) cc_final: 0.7991 (tpp)
REVERT: D  360 MET cc_start: 0.8433 (mtm) cc_final: 0.8161 (ttp)
REVERT: D  375 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8327 (mp0)
REVERT: A  177 MET cc_start: 0.1959 (mtp) cc_final: 0.1648 (mtp)
REVERT: A  266 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8563 (m-80)
  outliers start: 11
  outliers final: 7
  residues processed: 42
  average time/residue: 0.0827
  time to fit residues: 5.5983
Evaluate side-chains
  40 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  297 MET
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  478 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 105 optimal weight:    0.0670
   chunk 113 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 106 optimal weight:    0.3980
   chunk 96 optimal weight:    0.3980
   chunk 110 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 77 optimal weight:    0.4980
   chunk 69 optimal weight:   10.0000
   chunk 28 optimal weight:    0.4980
   overall best weight:    0.3718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.075749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.049635 restraints weight = 45008.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.049059 restraints weight = 30176.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.049337 restraints weight = 24625.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.049663 restraints weight = 21299.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.049757 restraints weight = 19606.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10105  Z= 0.087
  Angle     :  0.480   9.530  13755  Z= 0.240
  Chirality :  0.040   0.172   1494
  Planarity :  0.003   0.034   1760
  Dihedral  :  4.823  55.256   1458
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  9.83 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.25), residues: 1196
  helix:  2.09 (0.27), residues: 388
  sheet:  1.08 (0.40), residues: 155
  loop : -0.74 (0.25), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 646 
 TYR   0.014   0.001   TYR A 612 
 PHE   0.008   0.001   PHE D 369 
 TRP   0.011   0.001   TRP A 436 
 HIS   0.002   0.000   HIS D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 (10083)
  covalent geometry    : angle       0.47244 (13708)
  SS BOND              : bond        0.00127 (   13)
  SS BOND              : angle       0.39919 (   26)
  hydrogen bonds       : bond        0.03111 (  416)
  hydrogen bonds       : angle       4.21026 ( 1146)
  metal coordination   : bond        0.00051 (    2)
  link_NAG-ASN         : bond        0.00325 (    7)
  link_NAG-ASN         : angle       2.22060 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   97 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9239 (mm)
REVERT: D  152 MET cc_start: 0.8998 (tpp) cc_final: 0.8654 (tpt)
REVERT: D  190 MET cc_start: 0.9338 (ttp) cc_final: 0.9111 (tmm)
REVERT: D  270 MET cc_start: 0.8430 (tpp) cc_final: 0.7980 (tpp)
REVERT: D  360 MET cc_start: 0.8363 (mtm) cc_final: 0.8132 (ttp)
REVERT: D  375 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8260 (mp0)
REVERT: A  266 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8292 (m-80)
  outliers start: 9
  outliers final: 6
  residues processed: 39
  average time/residue: 0.0873
  time to fit residues: 5.4768
Evaluate side-chains
  39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  297 MET
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 96 optimal weight:    0.0060
   chunk 50 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 117 optimal weight:    0.7980
   chunk 58 optimal weight:   50.0000
   chunk 28 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0030
   chunk 33 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.4606

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.075718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.049632 restraints weight = 45163.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.049048 restraints weight = 30451.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.049343 restraints weight = 24664.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.049594 restraints weight = 21486.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.049787 restraints weight = 19897.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10105  Z= 0.090
  Angle     :  0.480  10.560  13755  Z= 0.239
  Chirality :  0.040   0.174   1494
  Planarity :  0.003   0.034   1760
  Dihedral  :  4.772  55.027   1458
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.30 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.25), residues: 1196
  helix:  2.09 (0.27), residues: 388
  sheet:  1.06 (0.40), residues: 155
  loop : -0.73 (0.25), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 245 
 TYR   0.015   0.001   TYR A 612 
 PHE   0.008   0.001   PHE D 369 
 TRP   0.009   0.001   TRP A 258 
 HIS   0.002   0.000   HIS D 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 (10083)
  covalent geometry    : angle       0.47295 (13708)
  SS BOND              : bond        0.00117 (   13)
  SS BOND              : angle       0.41112 (   26)
  hydrogen bonds       : bond        0.03053 (  416)
  hydrogen bonds       : angle       4.21608 ( 1146)
  metal coordination   : bond        0.00077 (    2)
  link_NAG-ASN         : bond        0.00296 (    7)
  link_NAG-ASN         : angle       2.19487 (   21)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   97 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9243 (mm)
REVERT: D  152 MET cc_start: 0.9003 (tpp) cc_final: 0.8682 (tpt)
REVERT: D  190 MET cc_start: 0.9351 (ttp) cc_final: 0.9117 (tmm)
REVERT: D  270 MET cc_start: 0.8392 (tpp) cc_final: 0.7942 (tpp)
REVERT: D  360 MET cc_start: 0.8328 (mtm) cc_final: 0.8027 (ttp)
REVERT: D  375 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8276 (mp0)
REVERT: A  177 MET cc_start: 0.1021 (mtp) cc_final: 0.0616 (mpp)
REVERT: A  266 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8280 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 38
  average time/residue: 0.0851
  time to fit residues: 5.1331
Evaluate side-chains
  40 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain D residue   98 GLN
Chi-restraints excluded: chain D residue  297 MET
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 81 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 113 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9990
   chunk 67 optimal weight:   30.0000
   chunk 70 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   chunk 103 optimal weight:    0.2980
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
D 239 HIS
D 340 GLN
A  49 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.073824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.044668 restraints weight = 46126.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.046629 restraints weight = 29749.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.046258 restraints weight = 18148.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.046565 restraints weight = 19615.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.046654 restraints weight = 16934.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  10105  Z= 0.257
  Angle     :  0.588  10.037  13755  Z= 0.303
  Chirality :  0.042   0.181   1494
  Planarity :  0.003   0.033   1760
  Dihedral  :  5.186  57.905   1458
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 10.11 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.25), residues: 1196
  helix:  1.69 (0.27), residues: 390
  sheet:  0.95 (0.39), residues: 167
  loop : -0.77 (0.25), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 454 
 TYR   0.027   0.002   TYR D 207 
 PHE   0.016   0.002   PHE D 452 
 TRP   0.009   0.001   TRP D 459 
 HIS   0.004   0.001   HIS D 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (10083)
  covalent geometry    : angle       0.58034 (13708)
  SS BOND              : bond        0.00244 (   13)
  SS BOND              : angle       0.81862 (   26)
  hydrogen bonds       : bond        0.04137 (  416)
  hydrogen bonds       : angle       4.61057 ( 1146)
  metal coordination   : bond        0.00371 (    2)
  link_NAG-ASN         : bond        0.00212 (    7)
  link_NAG-ASN         : angle       2.35296 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1606.05 seconds
wall clock time: 28 minutes 27.70 seconds (1707.70 seconds total)