Starting phenix.real_space_refine
on Tue Mar  3 13:00:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sl9_25195/03_2026/7sl9_25195_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sl9_25195/03_2026/7sl9_25195.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sl9_25195/03_2026/7sl9_25195.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sl9_25195/03_2026/7sl9_25195.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sl9_25195/03_2026/7sl9_25195_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sl9_25195/03_2026/7sl9_25195_neut.cif"
  }
  resolution = 3.5
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3091      2.51       5
     N     749      2.21       5
     O     844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  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: 4712
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3763
          Classifications: {'peptide': 497}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 19, 'TRANS': 477}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 943
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'BUA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.09, per 1000 atoms: 0.23
  Number of scatterers: 4712
  At special positions: 0
  Unit cell: (91.16, 77.38, 90.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     844      8.00
     N     749      7.00
     C    3091      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 480 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " 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
  Time building additional restraints: 0.41
  Conformation dependent library (CDL) restraints added in 378.2 milliseconds
  

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1120

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 3 sheets defined
      64.0% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 34
      removed outlier: 3.795A  pdb=" N   SER A  25 " --> pdb=" O   MET A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 66
      removed outlier: 3.529A  pdb=" N   ALA A  58 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A  59 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A  64 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 73
      removed outlier: 3.569A  pdb=" N   LEU A  72 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 82
      removed outlier: 3.815A  pdb=" N   ARG A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 86
    Processing helix  chain 'A' and resid 87 through 102
      removed outlier: 3.502A  pdb=" N   THR A  91 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE A  93 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 110
      removed outlier: 3.776A  pdb=" N   PHE A 107 " --> pdb=" O   PHE A 103 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU A 110 " --> pdb=" O   VAL A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 123
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.721A  pdb=" N   LEU A 129 " --> pdb=" O   LYS A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 159
      removed outlier: 3.689A  pdb=" N   GLY A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ILE A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      Proline residue:  A 150  - end of helix
      removed outlier: 4.035A  pdb=" N   GLN A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 175
      removed outlier: 3.880A  pdb=" N   VAL A 167 " --> pdb=" O   TRP A 163 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A 172 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   CYS A 173 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 212
      removed outlier: 3.991A  pdb=" N   PHE A 191 " --> pdb=" O   TRP A 187 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   GLN A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 193 " --> pdb=" O   ASP A 189 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA A 198 " --> pdb=" O   GLY A 194 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A 201 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN A 206 " --> pdb=" O   SER A 202 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 207 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 224
      removed outlier: 4.029A  pdb=" N   ASN A 219 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ALA A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   TYR A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 258
      removed outlier: 3.801A  pdb=" N   ILE A 245 " --> pdb=" O   THR A 241 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE A 251 " --> pdb=" O   ILE A 247 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   SER A 255 " --> pdb=" O   PHE A 251 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 256 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 263
    Processing helix  chain 'A' and resid 264 through 269
    Processing helix  chain 'A' and resid 272 through 305
      removed outlier: 3.652A  pdb=" N   LEU A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN A 283 " --> pdb=" O   SER A 279 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   VAL A 285 " --> pdb=" O   TYR A 281 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   CYS A 297 " --> pdb=" O   CYS A 293 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
      removed outlier: 3.510A  pdb=" N   GLN A 321 " --> pdb=" O   ALA A 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 318 through 321'
    Processing helix  chain 'A' and resid 322 through 331
      removed outlier: 3.622A  pdb=" N   LEU A 328 " --> pdb=" O   PRO A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 369
      removed outlier: 3.564A  pdb=" N   PHE A 341 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL A 342 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLY A 348 " --> pdb=" O   CYS A 344 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   THR A 349 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU A 350 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER A 354 " --> pdb=" O   LEU A 350 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL A 363 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR A 364 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE A 369 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 386
      removed outlier: 3.730A  pdb=" N   GLN A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 403
      removed outlier: 3.981A  pdb=" N   VAL A 390 " --> pdb=" O   GLN A 386 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 419
      removed outlier: 3.531A  pdb=" N   VAL A 416 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 433
      removed outlier: 3.846A  pdb=" N   LEU A 424 " --> pdb=" O   VAL A 420 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 427 " --> pdb=" O   PRO A 423 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   PHE A 428 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 463
      removed outlier: 3.787A  pdb=" N   VAL A 444 " --> pdb=" O   ILE A 440 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLN A 461 " --> pdb=" O   GLY A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 471
    Processing helix  chain 'A' and resid 510 through 516
    Processing helix  chain 'A' and resid 525 through 533
      removed outlier: 4.139A  pdb=" N   VAL A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 543
      removed outlier: 3.690A  pdb=" N   SER A 540 " --> pdb=" O   GLY A 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 66
      removed outlier: 4.051A  pdb=" N   LYS B  66 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9
      removed outlier: 3.775A  pdb=" N   THR B  79 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 41
      removed outlier: 3.741A  pdb=" N   ALA B  93 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 102
      removed outlier: 3.592A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 101 " (cutoff:3.500A)

    228 hydrogen bonds defined for protein.
    666 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.67

  Time building geometry restraints manager: 0.57 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: 1428
        1.34 -     1.46: 1175
        1.46 -     1.58: 2183
        1.58 -     1.70: 0
        1.70 -     1.81: 43
  Bond restraints: 4829
  Sorted by residual:
  bond pdb=" C   THR A 510 "
       pdb=" N   PRO A 511 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.023 1.08e-02 8.57e+03 4.38e+00
  bond pdb=" C   SER A 317 "
       pdb=" N   ALA A 318 "
    ideal  model  delta    sigma   weight residual
    1.329  1.276  0.052 3.03e-02 1.09e+03 2.99e+00
  bond pdb=" C3  BUA A 701 "
       pdb=" C4  BUA A 701 "
    ideal  model  delta    sigma   weight residual
    1.539  1.506  0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" N   LYS A 314 "
       pdb=" CA  LYS A 314 "
    ideal  model  delta    sigma   weight residual
    1.460  1.485 -0.024 1.51e-02 4.39e+03 2.58e+00
  bond pdb=" N   VAL A 316 "
       pdb=" CA  VAL A 316 "
    ideal  model  delta    sigma   weight residual
    1.458  1.440  0.018 1.19e-02 7.06e+03 2.39e+00
  ... (remaining 4824 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 6398
        2.36 -     4.71: 153
        4.71 -     7.07: 31
        7.07 -     9.42: 8
        9.42 -    11.78: 2
  Bond angle restraints: 6592
  Sorted by residual:
  angle pdb=" N   LYS A 315 "
        pdb=" CA  LYS A 315 "
        pdb=" C   LYS A 315 "
      ideal   model   delta    sigma   weight residual
     110.35  122.13  -11.78 1.36e+00 5.41e-01 7.50e+01
  angle pdb=" N   VAL A 316 "
        pdb=" CA  VAL A 316 "
        pdb=" C   VAL A 316 "
      ideal   model   delta    sigma   weight residual
     108.12   98.81    9.31 1.44e+00 4.82e-01 4.18e+01
  angle pdb=" N   GLN A 508 "
        pdb=" CA  GLN A 508 "
        pdb=" C   GLN A 508 "
      ideal   model   delta    sigma   weight residual
     112.68  107.28    5.40 1.33e+00 5.65e-01 1.65e+01
  angle pdb=" C   PHE A 160 "
        pdb=" N   ASP A 161 "
        pdb=" CA  ASP A 161 "
      ideal   model   delta    sigma   weight residual
     121.54  129.16   -7.62 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" C   THR A 178 "
        pdb=" N   LEU A 179 "
        pdb=" CA  LEU A 179 "
      ideal   model   delta    sigma   weight residual
     124.31  130.91   -6.60 1.67e+00 3.59e-01 1.56e+01
  ... (remaining 6587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 2473
       17.66 -    35.32: 236
       35.32 -    52.98: 36
       52.98 -    70.64: 7
       70.64 -    88.30: 2
  Dihedral angle restraints: 2754
    sinusoidal: 983
      harmonic: 1771
  Sorted by residual:
  dihedral pdb=" CA  TYR B 111 "
           pdb=" C   TYR B 111 "
           pdb=" N   TYR B 112 "
           pdb=" CA  TYR B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.42  -29.58     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  LEU A 409 "
           pdb=" C   LEU A 409 "
           pdb=" N   LEU A 410 "
           pdb=" CA  LEU A 410 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.76   22.24     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  ILE A 477 "
           pdb=" C   ILE A 477 "
           pdb=" N   GLN A 478 "
           pdb=" CA  GLN A 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.94  -22.06     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 2751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 695
       0.092 -    0.184: 67
       0.184 -    0.276: 6
       0.276 -    0.368: 0
       0.368 -    0.460: 1
  Chirality restraints: 769
  Sorted by residual:
  chirality pdb=" CA  LYS A 315 "
            pdb=" N   LYS A 315 "
            pdb=" C   LYS A 315 "
            pdb=" CB  LYS A 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.29e+00
  chirality pdb=" CA  VAL A 316 "
            pdb=" N   VAL A 316 "
            pdb=" C   VAL A 316 "
            pdb=" CB  VAL A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CB  VAL A 203 "
            pdb=" CA  VAL A 203 "
            pdb=" CG1 VAL A 203 "
            pdb=" CG2 VAL A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 766 not shown)

  Planarity restraints: 813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  BUA A 701 "   -0.019 2.00e-02 2.50e+03   3.90e-02 1.52e+01
        pdb=" C4  BUA A 701 "    0.067 2.00e-02 2.50e+03
        pdb=" O1  BUA A 701 "   -0.024 2.00e-02 2.50e+03
        pdb=" O2  BUA A 701 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 309 "   -0.040 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO A 310 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 310 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 310 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 422 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO A 423 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 423 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 423 "    0.032 5.00e-02 4.00e+02
  ... (remaining 810 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1296
        2.79 -     3.32: 4351
        3.32 -     3.84: 7690
        3.84 -     4.37: 9146
        4.37 -     4.90: 15370
  Nonbonded interactions: 37853
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 472 "
            pdb=" OH  TYR B 111 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OG1 THR B  92 "
            pdb=" O   VAL B 120 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   GLY A 224 "
            pdb=" OG  SER B  31 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   ILE A 246 "
            pdb=" OG1 THR A 250 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   THR A 250 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.312 3.040
  ... (remaining 37848 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:             0.790
  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:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.460
  Find NCS groups from input model:        0.010
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
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      :  0.005   0.060   4831  Z= 0.225
  Angle     :  0.951  11.781   6596  Z= 0.523
  Chirality :  0.058   0.460    769
  Planarity :  0.007   0.061    813
  Dihedral  : 13.950  88.296   1628
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  9.51 %
    Favored  : 90.08 %
  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: -6.01 (0.22), residues: 611
  helix: -4.33 (0.11), residues: 357
  sheet: -2.43 (0.71), residues: 45
  loop : -3.26 (0.35), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 266 
 TYR   0.015   0.002   TYR A 372 
 PHE   0.019   0.002   PHE A 160 
 TRP   0.031   0.002   TRP A 516 
 HIS   0.004   0.002   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 4829)
  covalent geometry    : angle       0.95096 ( 6592)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       1.10863 (    4)
  hydrogen bonds       : bond        0.30851 (  228)
  hydrogen bonds       : angle      11.09135 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 PHE cc_start: 0.9162 (t80) cc_final: 0.8863 (t80)
REVERT: A  277 LYS cc_start: 0.8937 (mttt) cc_final: 0.8592 (mttp)
REVERT: A  383 TRP cc_start: 0.7797 (t60) cc_final: 0.7558 (t60)
REVERT: A  425 MET cc_start: 0.9033 (tmm) cc_final: 0.8480 (ttt)
REVERT: A  480 CYS cc_start: 0.5398 (t) cc_final: 0.5137 (t)
REVERT: A  514 ASP cc_start: 0.8187 (t0) cc_final: 0.7854 (m-30)
REVERT: A  515 ASN cc_start: 0.8798 (m-40) cc_final: 0.8590 (m-40)
REVERT: B    6 LEU cc_start: 0.8717 (pt) cc_final: 0.8467 (pp)
REVERT: B   39 TYR cc_start: 0.8364 (m-80) cc_final: 0.8008 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 163
  average time/residue: 0.0630
  time to fit residues: 13.3903
Evaluate side-chains
  129 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.0980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 156 GLN
A 474 HIS
B   5 GLN
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.145799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.106988 restraints weight = 7601.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.110658 restraints weight = 3888.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.112996 restraints weight = 2674.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.114351 restraints weight = 2175.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.114944 restraints weight = 1946.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4831  Z= 0.138
  Angle     :  0.702  12.142   6596  Z= 0.358
  Chirality :  0.044   0.193    769
  Planarity :  0.005   0.042    813
  Dihedral  :  5.605  26.532    672
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.62 %
    Favored  : 78.14 %
  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: -4.06 (0.27), residues: 611
  helix: -2.42 (0.20), residues: 363
  sheet: -3.16 (0.65), residues: 47
  loop : -2.71 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  47 
 TYR   0.015   0.001   TYR A 302 
 PHE   0.012   0.001   PHE B  69 
 TRP   0.014   0.001   TRP A 516 
 HIS   0.002   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4829)
  covalent geometry    : angle       0.70251 ( 6592)
  SS BOND              : bond        0.00016 (    2)
  SS BOND              : angle       0.56425 (    4)
  hydrogen bonds       : bond        0.04106 (  228)
  hydrogen bonds       : angle       5.58372 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.7820 (mmt) cc_final: 0.7566 (mmm)
REVERT: A   66 MET cc_start: 0.8162 (tpp) cc_final: 0.7889 (tpp)
REVERT: A  125 LYS cc_start: 0.8896 (tptp) cc_final: 0.8497 (tptp)
REVERT: A  191 PHE cc_start: 0.9267 (t80) cc_final: 0.9029 (t80)
REVERT: A  383 TRP cc_start: 0.7597 (t60) cc_final: 0.7310 (t60)
REVERT: B    6 LEU cc_start: 0.8738 (pt) cc_final: 0.8513 (pp)
REVERT: B   21 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8907 (mmm-85)
REVERT: B   54 ASN cc_start: 0.8950 (p0) cc_final: 0.8339 (p0)
REVERT: B   61 TYR cc_start: 0.8850 (m-80) cc_final: 0.8516 (m-80)
REVERT: B   68 ARG cc_start: 0.7429 (ptm160) cc_final: 0.6873 (ptm160)
REVERT: B   69 PHE cc_start: 0.8195 (m-10) cc_final: 0.7942 (m-80)
REVERT: B   82 LEU cc_start: 0.9505 (tt) cc_final: 0.9146 (tt)
REVERT: B   84 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7221 (mmp)
REVERT: B   91 ASP cc_start: 0.7353 (p0) cc_final: 0.7085 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 151
  average time/residue: 0.0576
  time to fit residues: 11.5792
Evaluate side-chains
  135 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 TYR
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 39 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.150358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.112158 restraints weight = 7696.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.115961 restraints weight = 3991.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.118473 restraints weight = 2738.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.119942 restraints weight = 2205.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.120584 restraints weight = 1954.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4831  Z= 0.131
  Angle     :  0.676  10.785   6596  Z= 0.335
  Chirality :  0.042   0.141    769
  Planarity :  0.004   0.035    813
  Dihedral  :  5.123  24.104    672
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.26 %
    Favored  : 74.90 %
  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: -2.97 (0.31), residues: 611
  helix: -1.43 (0.24), residues: 372
  sheet: -3.14 (0.63), residues: 45
  loop : -2.42 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  47 
 TYR   0.014   0.001   TYR A 176 
 PHE   0.012   0.001   PHE A 436 
 TRP   0.009   0.001   TRP A 516 
 HIS   0.002   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4829)
  covalent geometry    : angle       0.67574 ( 6592)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.48230 (    4)
  hydrogen bonds       : bond        0.03584 (  228)
  hydrogen bonds       : angle       5.04159 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.7820 (mmt) cc_final: 0.7606 (mmm)
REVERT: A   31 TYR cc_start: 0.8667 (t80) cc_final: 0.8429 (t80)
REVERT: A   52 MET cc_start: 0.7198 (mmm) cc_final: 0.6866 (mmm)
REVERT: A  219 ASN cc_start: 0.8416 (t0) cc_final: 0.8017 (t0)
REVERT: A  383 TRP cc_start: 0.7543 (t60) cc_final: 0.7253 (t60)
REVERT: B   21 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8812 (tpp80)
REVERT: B   48 GLU cc_start: 0.8216 (tt0) cc_final: 0.7931 (tt0)
REVERT: B   53 ILE cc_start: 0.8080 (pt) cc_final: 0.7803 (pt)
REVERT: B   54 ASN cc_start: 0.8919 (p0) cc_final: 0.8210 (p0)
REVERT: B   82 LEU cc_start: 0.9420 (tt) cc_final: 0.8020 (tp)
REVERT: B  109 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7065 (p0)
  outliers start: 19
  outliers final: 13
  residues processed: 145
  average time/residue: 0.0569
  time to fit residues: 10.7983
Evaluate side-chains
  142 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 57 optimal weight:    0.2980
   chunk 0 optimal weight:    8.9990
   chunk 60 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.150981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.112493 restraints weight = 7677.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.116239 restraints weight = 4002.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118855 restraints weight = 2757.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.120310 restraints weight = 2207.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.120891 restraints weight = 1956.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4831  Z= 0.128
  Angle     :  0.683  10.884   6596  Z= 0.336
  Chirality :  0.042   0.130    769
  Planarity :  0.004   0.036    813
  Dihedral  :  5.052  23.883    672
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 21.26 %
    Favored  : 73.48 %
  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: -2.36 (0.32), residues: 611
  helix: -0.88 (0.25), residues: 373
  sheet: -2.95 (0.67), residues: 47
  loop : -2.31 (0.44), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  47 
 TYR   0.022   0.001   TYR B  61 
 PHE   0.024   0.001   PHE A  65 
 TRP   0.006   0.001   TRP A 516 
 HIS   0.002   0.001   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4829)
  covalent geometry    : angle       0.68346 ( 6592)
  SS BOND              : bond        0.00104 (    2)
  SS BOND              : angle       0.39927 (    4)
  hydrogen bonds       : bond        0.03301 (  228)
  hydrogen bonds       : angle       4.78640 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ASN cc_start: 0.8425 (t0) cc_final: 0.8007 (t0)
REVERT: A  282 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8956 (mm)
REVERT: A  383 TRP cc_start: 0.7587 (t60) cc_final: 0.7336 (t60)
REVERT: B   21 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8869 (tpp80)
REVERT: B   54 ASN cc_start: 0.8875 (p0) cc_final: 0.8240 (p0)
REVERT: B   82 LEU cc_start: 0.9347 (tt) cc_final: 0.9007 (tp)
REVERT: B  109 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7063 (p0)
  outliers start: 26
  outliers final: 21
  residues processed: 150
  average time/residue: 0.0624
  time to fit residues: 12.3904
Evaluate side-chains
  150 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 55 optimal weight:   10.0000
   chunk 1 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B  29 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.149747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.109702 restraints weight = 7674.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.113350 restraints weight = 4107.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.115800 restraints weight = 2877.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.116875 restraints weight = 2356.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.117991 restraints weight = 2132.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4831  Z= 0.157
  Angle     :  0.704   9.307   6596  Z= 0.347
  Chirality :  0.043   0.130    769
  Planarity :  0.004   0.038    813
  Dihedral  :  5.123  24.946    672
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 21.05 %
    Favored  : 72.47 %
  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: -1.98 (0.34), residues: 611
  helix: -0.51 (0.27), residues: 371
  sheet: -3.04 (0.69), residues: 49
  loop : -2.22 (0.44), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  68 
 TYR   0.013   0.001   TYR A  32 
 PHE   0.024   0.001   PHE A  65 
 TRP   0.005   0.001   TRP A 311 
 HIS   0.002   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 4829)
  covalent geometry    : angle       0.70373 ( 6592)
  SS BOND              : bond        0.00114 (    2)
  SS BOND              : angle       0.32821 (    4)
  hydrogen bonds       : bond        0.03275 (  228)
  hydrogen bonds       : angle       4.75594 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 138
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8997 (tptp) cc_final: 0.8606 (tptp)
REVERT: A  219 ASN cc_start: 0.8397 (t0) cc_final: 0.8017 (t0)
REVERT: A  383 TRP cc_start: 0.7630 (t60) cc_final: 0.7357 (t60)
REVERT: B   21 ARG cc_start: 0.9098 (ttp80) cc_final: 0.8865 (tpp80)
REVERT: B   54 ASN cc_start: 0.8888 (p0) cc_final: 0.8189 (p0)
REVERT: B   68 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7412 (ptm160)
REVERT: B   69 PHE cc_start: 0.8633 (m-80) cc_final: 0.7853 (m-80)
REVERT: B   82 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8849 (tt)
REVERT: B   91 ASP cc_start: 0.7083 (p0) cc_final: 0.6638 (p0)
  outliers start: 32
  outliers final: 25
  residues processed: 157
  average time/residue: 0.0568
  time to fit residues: 12.0316
Evaluate side-chains
  152 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 50 optimal weight:   30.0000
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 35 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.150027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.110126 restraints weight = 7738.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.113840 restraints weight = 4144.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.116204 restraints weight = 2895.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.117496 restraints weight = 2364.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.118109 restraints weight = 2122.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4831  Z= 0.148
  Angle     :  0.704   8.765   6596  Z= 0.349
  Chirality :  0.043   0.129    769
  Planarity :  0.004   0.035    813
  Dihedral  :  5.114  24.677    672
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 21.26 %
    Favored  : 72.47 %
  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: -1.78 (0.34), residues: 611
  helix: -0.37 (0.27), residues: 371
  sheet: -2.96 (0.71), residues: 47
  loop : -2.11 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  68 
 TYR   0.019   0.001   TYR A  32 
 PHE   0.028   0.001   PHE A 160 
 TRP   0.005   0.001   TRP A 311 
 HIS   0.002   0.001   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4829)
  covalent geometry    : angle       0.70380 ( 6592)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       0.26312 (    4)
  hydrogen bonds       : bond        0.03218 (  228)
  hydrogen bonds       : angle       4.70636 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8976 (tptp) cc_final: 0.8742 (tptp)
REVERT: A  219 ASN cc_start: 0.8438 (t0) cc_final: 0.8057 (t0)
REVERT: A  290 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8838 (tt)
REVERT: A  383 TRP cc_start: 0.7653 (t60) cc_final: 0.7363 (t60)
REVERT: B   21 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8851 (tpp80)
REVERT: B   54 ASN cc_start: 0.8855 (p0) cc_final: 0.8210 (p0)
REVERT: B   82 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8810 (tp)
REVERT: B  109 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.6983 (p0)
  outliers start: 31
  outliers final: 24
  residues processed: 155
  average time/residue: 0.0508
  time to fit residues: 10.5207
Evaluate side-chains
  159 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B   5 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.152656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.112360 restraints weight = 7700.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.116103 restraints weight = 4133.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.118559 restraints weight = 2894.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.119770 restraints weight = 2361.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.120603 restraints weight = 2120.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4831  Z= 0.134
  Angle     :  0.712  10.118   6596  Z= 0.349
  Chirality :  0.043   0.130    769
  Planarity :  0.004   0.036    813
  Dihedral  :  5.123  29.870    672
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 22.87 %
    Favored  : 71.05 %
  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: -1.71 (0.34), residues: 611
  helix: -0.25 (0.27), residues: 371
  sheet: -3.10 (0.67), residues: 49
  loop : -2.15 (0.46), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  68 
 TYR   0.018   0.001   TYR A  32 
 PHE   0.034   0.001   PHE A  65 
 TRP   0.004   0.001   TRP A 516 
 HIS   0.002   0.001   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4829)
  covalent geometry    : angle       0.71241 ( 6592)
  SS BOND              : bond        0.00086 (    2)
  SS BOND              : angle       0.30650 (    4)
  hydrogen bonds       : bond        0.03106 (  228)
  hydrogen bonds       : angle       4.66959 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8954 (tptp) cc_final: 0.8564 (tptp)
REVERT: A  219 ASN cc_start: 0.8403 (t0) cc_final: 0.8012 (t0)
REVERT: A  383 TRP cc_start: 0.7645 (t60) cc_final: 0.7368 (t60)
REVERT: B   53 ILE cc_start: 0.7747 (pt) cc_final: 0.7438 (pt)
REVERT: B   54 ASN cc_start: 0.8949 (p0) cc_final: 0.8267 (p0)
REVERT: B   69 PHE cc_start: 0.8539 (m-80) cc_final: 0.8148 (m-10)
REVERT: B   82 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8588 (tp)
REVERT: B  109 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6923 (p0)
  outliers start: 30
  outliers final: 25
  residues processed: 145
  average time/residue: 0.0500
  time to fit residues: 9.6637
Evaluate side-chains
  147 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  513 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:    8.9990
   chunk 21 optimal weight:    0.1980
   chunk 57 optimal weight:    0.0570
   chunk 35 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
B   5 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.154084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.114176 restraints weight = 7773.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.118037 restraints weight = 4117.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.120588 restraints weight = 2859.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.122078 restraints weight = 2317.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.122743 restraints weight = 2060.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4831  Z= 0.125
  Angle     :  0.701   9.040   6596  Z= 0.346
  Chirality :  0.042   0.122    769
  Planarity :  0.004   0.037    813
  Dihedral  :  4.973  28.739    672
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.89 %
    Favored  : 70.85 %
  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: -1.59 (0.34), residues: 611
  helix: -0.18 (0.27), residues: 371
  sheet: -2.89 (0.66), residues: 49
  loop : -2.12 (0.46), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  68 
 TYR   0.017   0.001   TYR A 176 
 PHE   0.029   0.001   PHE A  65 
 TRP   0.008   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4829)
  covalent geometry    : angle       0.70111 ( 6592)
  SS BOND              : bond        0.00071 (    2)
  SS BOND              : angle       0.35045 (    4)
  hydrogen bonds       : bond        0.03094 (  228)
  hydrogen bonds       : angle       4.61381 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8865 (tptp) cc_final: 0.8392 (tptp)
REVERT: A  219 ASN cc_start: 0.8297 (t0) cc_final: 0.7952 (t0)
REVERT: A  277 LYS cc_start: 0.8958 (mttt) cc_final: 0.8743 (mttt)
REVERT: A  341 PHE cc_start: 0.8031 (t80) cc_final: 0.7785 (t80)
REVERT: B   21 ARG cc_start: 0.8731 (tpp80) cc_final: 0.8432 (tpp80)
REVERT: B   54 ASN cc_start: 0.8895 (p0) cc_final: 0.8278 (p0)
REVERT: B   69 PHE cc_start: 0.8540 (m-80) cc_final: 0.8258 (m-80)
REVERT: B  109 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6923 (p0)
  outliers start: 26
  outliers final: 20
  residues processed: 148
  average time/residue: 0.0563
  time to fit residues: 11.0478
Evaluate side-chains
  149 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:   20.0000
   chunk 20 optimal weight:    0.0670
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.152119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.112024 restraints weight = 7665.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.115876 restraints weight = 4143.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.118346 restraints weight = 2899.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.119684 restraints weight = 2366.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.120357 restraints weight = 2118.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4831  Z= 0.134
  Angle     :  0.725   9.030   6596  Z= 0.356
  Chirality :  0.043   0.145    769
  Planarity :  0.004   0.038    813
  Dihedral  :  4.998  28.619    672
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 24.70 %
    Favored  : 70.04 %
  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: -1.56 (0.34), residues: 611
  helix: -0.15 (0.27), residues: 373
  sheet: -2.85 (0.62), residues: 54
  loop : -2.09 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  68 
 TYR   0.014   0.001   TYR A  32 
 PHE   0.035   0.001   PHE A 160 
 TRP   0.013   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 306 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4829)
  covalent geometry    : angle       0.72535 ( 6592)
  SS BOND              : bond        0.00089 (    2)
  SS BOND              : angle       0.29129 (    4)
  hydrogen bonds       : bond        0.03097 (  228)
  hydrogen bonds       : angle       4.64361 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8856 (tptp) cc_final: 0.8446 (tptp)
REVERT: A  219 ASN cc_start: 0.8298 (t0) cc_final: 0.7919 (t0)
REVERT: A  277 LYS cc_start: 0.8926 (mttt) cc_final: 0.8642 (mttt)
REVERT: A  281 TYR cc_start: 0.8673 (m-80) cc_final: 0.8423 (m-80)
REVERT: A  341 PHE cc_start: 0.8067 (t80) cc_final: 0.7795 (t80)
REVERT: A  383 TRP cc_start: 0.7625 (t60) cc_final: 0.7339 (t60)
REVERT: B   20 LEU cc_start: 0.8723 (tt) cc_final: 0.8431 (mm)
REVERT: B   21 ARG cc_start: 0.8761 (tpp80) cc_final: 0.8364 (tpp80)
REVERT: B   32 THR cc_start: 0.9077 (p) cc_final: 0.8865 (p)
REVERT: B   54 ASN cc_start: 0.8930 (p0) cc_final: 0.8293 (p0)
REVERT: B   68 ARG cc_start: 0.7897 (ttp-110) cc_final: 0.7535 (ptm160)
REVERT: B   69 PHE cc_start: 0.8525 (m-80) cc_final: 0.8073 (m-80)
REVERT: B   91 ASP cc_start: 0.6655 (p0) cc_final: 0.6300 (p0)
REVERT: B  109 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6941 (p0)
  outliers start: 26
  outliers final: 23
  residues processed: 142
  average time/residue: 0.0583
  time to fit residues: 10.9921
Evaluate side-chains
  147 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   36 MET
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.143453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.104711 restraints weight = 7341.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.108270 restraints weight = 3963.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.110681 restraints weight = 2745.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111774 restraints weight = 2211.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.112884 restraints weight = 1980.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4831  Z= 0.212
  Angle     :  0.781   8.460   6596  Z= 0.387
  Chirality :  0.046   0.144    769
  Planarity :  0.004   0.039    813
  Dihedral  :  5.322  29.051    672
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 25.91 %
    Favored  : 69.84 %
  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: -1.47 (0.35), residues: 611
  helix: -0.12 (0.28), residues: 364
  sheet: -2.54 (0.65), residues: 52
  loop : -1.97 (0.47), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  68 
 TYR   0.018   0.001   TYR A 176 
 PHE   0.031   0.002   PHE A 160 
 TRP   0.011   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 4829)
  covalent geometry    : angle       0.78146 ( 6592)
  SS BOND              : bond        0.00154 (    2)
  SS BOND              : angle       0.48142 (    4)
  hydrogen bonds       : bond        0.03462 (  228)
  hydrogen bonds       : angle       4.90874 (  666)

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

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

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1222 Ramachandran restraints generated.
    611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8908 (tptp) cc_final: 0.8492 (tptp)
REVERT: A  219 ASN cc_start: 0.8455 (t0) cc_final: 0.7898 (t0)
REVERT: A  277 LYS cc_start: 0.8914 (mttt) cc_final: 0.8606 (mttp)
REVERT: A  281 TYR cc_start: 0.8752 (m-80) cc_final: 0.8453 (m-80)
REVERT: B   21 ARG cc_start: 0.8770 (tpp80) cc_final: 0.8513 (tpp80)
REVERT: B   54 ASN cc_start: 0.8930 (p0) cc_final: 0.8226 (p0)
REVERT: B   69 PHE cc_start: 0.8473 (m-80) cc_final: 0.8100 (m-80)
  outliers start: 21
  outliers final: 16
  residues processed: 135
  average time/residue: 0.0593
  time to fit residues: 10.6087
Evaluate side-chains
  129 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   49 PHE
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 36 optimal weight:    8.9990
   chunk 23 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.152337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.111871 restraints weight = 7720.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115613 restraints weight = 4151.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.117810 restraints weight = 2911.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.119476 restraints weight = 2403.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.120031 restraints weight = 2124.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4831  Z= 0.148
  Angle     :  0.753   9.099   6596  Z= 0.370
  Chirality :  0.044   0.137    769
  Planarity :  0.004   0.043    813
  Dihedral  :  5.123  28.318    672
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 26.11 %
    Favored  : 70.04 %
  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: -1.42 (0.35), residues: 611
  helix: -0.07 (0.28), residues: 365
  sheet: -2.80 (0.62), residues: 52
  loop : -1.91 (0.47), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  47 
 TYR   0.012   0.001   TYR A 302 
 PHE   0.036   0.001   PHE A 160 
 TRP   0.008   0.001   TRP A 311 
 HIS   0.002   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 4829)
  covalent geometry    : angle       0.75290 ( 6592)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       0.34928 (    4)
  hydrogen bonds       : bond        0.03205 (  228)
  hydrogen bonds       : angle       4.80903 (  666)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 955.26 seconds
wall clock time: 17 minutes 6.73 seconds (1026.73 seconds total)