Starting phenix.real_space_refine
on Tue Feb 11 07:49:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sl9_25195/02_2025/7sl9_25195_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sl9_25195/02_2025/7sl9_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_25195/02_2025/7sl9_25195.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sl9_25195/02_2025/7sl9_25195.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sl9_25195/02_2025/7sl9_25195_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sl9_25195/02_2025/7sl9_25195_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 2, 'ARG:plan': 1, '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: 3.19, per 1000 atoms: 0.68
  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: 1.08
  Conformation dependent library (CDL) restraints added in 749.7 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: 0.61
  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: 1.33

  Time building geometry restraints manager: 1.26 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:             0.630
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.070
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.790
-------------------------------------------------------------------------------
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   4829  Z= 0.308
  Angle     :  0.951  11.781   6592  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 : 4.68
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.031   0.002   TRP A 516 
 HIS   0.004   0.002   HIS A 306 
 PHE   0.019   0.002   PHE A 160 
 TYR   0.015   0.002   TYR A 372 
 ARG   0.002   0.000   ARG A 266 

*********************** 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  : 0.483 
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: 0.8591 (mttp)
REVERT: A  383 TRP cc_start: 0.7797 (t60) cc_final: 0.7559 (t60)
REVERT: A  425 MET cc_start: 0.9033 (tmm) cc_final: 0.8483 (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: 0.8466 (pp)
REVERT: B   21 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8850 (ttp80)
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: 0.1487
  time to fit residues: 31.2777
Evaluate side-chains
  128 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
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 51 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 25 optimal weight:    0.3980
   chunk 15 optimal weight:    8.9990
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 156 GLN
A 474 HIS
B   5 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.146276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.107529 restraints weight = 7544.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.111270 restraints weight = 3853.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.113624 restraints weight = 2640.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
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   0.031   4829  Z= 0.188
  Angle     :  0.697  11.585   6592  Z= 0.356
  Chirality :  0.043   0.190    769
  Planarity :  0.005   0.042    813
  Dihedral  :  5.606  26.571    672
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 9.35
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.08 (0.27), residues: 611
  helix: -2.44 (0.20), residues: 364
  sheet: -3.15 (0.65), residues: 47
  loop : -2.71 (0.39), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 516 
 HIS   0.002   0.001   HIS A 474 
 PHE   0.011   0.001   PHE B  69 
 TYR   0.014   0.001   TYR A 108 
 ARG   0.005   0.000   ARG B  47 

*********************** 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
  160 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.7848 (mmt) cc_final: 0.7599 (mmm)
REVERT: A   66 MET cc_start: 0.8168 (tpp) cc_final: 0.7893 (tpp)
REVERT: A  125 LYS cc_start: 0.8888 (tptp) cc_final: 0.8487 (tptp)
REVERT: A  383 TRP cc_start: 0.7619 (t60) cc_final: 0.7330 (t60)
REVERT: B    6 LEU cc_start: 0.8738 (pt) cc_final: 0.8516 (pp)
REVERT: B   21 ARG cc_start: 0.9100 (ttp80) cc_final: 0.8681 (ttm-80)
REVERT: B   54 ASN cc_start: 0.8957 (p0) cc_final: 0.8332 (p0)
REVERT: B   61 TYR cc_start: 0.8822 (m-80) cc_final: 0.8497 (m-80)
REVERT: B   68 ARG cc_start: 0.7467 (ptm160) cc_final: 0.6880 (ptm160)
REVERT: B   69 PHE cc_start: 0.8226 (m-10) cc_final: 0.7966 (m-80)
REVERT: B   82 LEU cc_start: 0.9476 (tt) cc_final: 0.9061 (tt)
REVERT: B   84 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7277 (mmp)
REVERT: B   91 ASP cc_start: 0.7356 (p0) cc_final: 0.7086 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 150
  average time/residue: 0.1490
  time to fit residues: 29.2817
Evaluate side-chains
  133 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
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 49 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 44 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.144024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.104111 restraints weight = 7722.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.107713 restraints weight = 4125.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.110126 restraints weight = 2911.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   4829  Z= 0.373
  Angle     :  0.752  11.036   6592  Z= 0.379
  Chirality :  0.046   0.152    769
  Planarity :  0.004   0.034    813
  Dihedral  :  5.600  27.647    672
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 19.03 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.31), residues: 611
  helix: -1.35 (0.24), residues: 365
  sheet: -3.29 (0.62), residues: 47
  loop : -2.45 (0.41), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 243 
 HIS   0.004   0.001   HIS A 240 
 PHE   0.013   0.001   PHE A 296 
 TYR   0.013   0.002   TYR A 176 
 ARG   0.005   0.000   ARG B  47 

*********************** 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
  154 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.7880 (mmt) cc_final: 0.7679 (mmm)
REVERT: A   31 TYR cc_start: 0.8813 (t80) cc_final: 0.8602 (t80)
REVERT: A  125 LYS cc_start: 0.8876 (tptp) cc_final: 0.8621 (tptp)
REVERT: A  383 TRP cc_start: 0.7762 (t60) cc_final: 0.7538 (t60)
REVERT: B    6 LEU cc_start: 0.8742 (pt) cc_final: 0.8534 (pp)
REVERT: B   21 ARG cc_start: 0.9105 (ttp80) cc_final: 0.8717 (ttm-80)
REVERT: B   48 GLU cc_start: 0.8263 (tt0) cc_final: 0.7787 (tt0)
REVERT: B   54 ASN cc_start: 0.8978 (p0) cc_final: 0.8415 (p0)
REVERT: B   68 ARG cc_start: 0.7537 (ptm160) cc_final: 0.6958 (ptm160)
REVERT: B   82 LEU cc_start: 0.9479 (tt) cc_final: 0.9217 (tt)
REVERT: B   91 ASP cc_start: 0.7348 (p0) cc_final: 0.7035 (p0)
REVERT: B   95 TYR cc_start: 0.8715 (m-10) cc_final: 0.8420 (m-10)
  outliers start: 32
  outliers final: 24
  residues processed: 140
  average time/residue: 0.1588
  time to fit residues: 28.9007
Evaluate side-chains
  139 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   15 TYR
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  167 VAL
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  307 ASP
Chi-restraints excluded: chain A residue  330 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  510 THR
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   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 8 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0010
   chunk 30 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0970
   chunk 44 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
B  29 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.150182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.111028 restraints weight = 7740.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.114839 restraints weight = 4075.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.117325 restraints weight = 2822.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4829  Z= 0.170
  Angle     :  0.679  11.157   6592  Z= 0.334
  Chirality :  0.041   0.132    769
  Planarity :  0.004   0.035    813
  Dihedral  :  5.147  24.547    672
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 22.47 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.32), residues: 611
  helix: -0.91 (0.25), residues: 372
  sheet: -3.04 (0.66), residues: 47
  loop : -2.30 (0.44), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 253 
 HIS   0.002   0.001   HIS A 306 
 PHE   0.009   0.001   PHE B  69 
 TYR   0.011   0.001   TYR A 302 
 ARG   0.005   0.000   ARG B  47 

*********************** 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: 21
    poor density    : 141
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.7784 (mmt) cc_final: 0.7558 (mmm)
REVERT: A  219 ASN cc_start: 0.8440 (t0) cc_final: 0.8035 (t0)
REVERT: A  282 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8859 (mm)
REVERT: A  383 TRP cc_start: 0.7675 (t60) cc_final: 0.7375 (t60)
REVERT: B   21 ARG cc_start: 0.9125 (ttp80) cc_final: 0.8715 (tpp80)
REVERT: B   29 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8853 (p0)
REVERT: B   54 ASN cc_start: 0.8872 (p0) cc_final: 0.8230 (p0)
REVERT: B   82 LEU cc_start: 0.9384 (tt) cc_final: 0.8934 (tt)
REVERT: B   95 TYR cc_start: 0.8482 (m-10) cc_final: 0.8180 (m-10)
REVERT: B  109 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.6980 (p0)
  outliers start: 21
  outliers final: 13
  residues processed: 150
  average time/residue: 0.1433
  time to fit residues: 28.6895
Evaluate side-chains
  145 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  337 LEU
Chi-restraints excluded: chain A residue  430 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   29 ASN
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 35 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.147776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.107877 restraints weight = 7796.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.111529 restraints weight = 4141.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.113964 restraints weight = 2898.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4829  Z= 0.250
  Angle     :  0.727  11.895   6592  Z= 0.358
  Chirality :  0.044   0.129    769
  Planarity :  0.004   0.032    813
  Dihedral  :  5.214  25.668    672
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 21.05 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.34), residues: 611
  helix: -0.52 (0.26), residues: 371
  sheet: -2.94 (0.71), residues: 47
  loop : -2.16 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 243 
 HIS   0.002   0.001   HIS A 240 
 PHE   0.013   0.001   PHE A  65 
 TYR   0.013   0.001   TYR A  32 
 ARG   0.007   0.000   ARG B  68 

*********************** 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
  167 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LYS cc_start: 0.8878 (tptp) cc_final: 0.8502 (tptp)
REVERT: A  219 ASN cc_start: 0.8487 (t0) cc_final: 0.8050 (t0)
REVERT: A  383 TRP cc_start: 0.7716 (t60) cc_final: 0.7427 (t60)
REVERT: A  436 PHE cc_start: 0.7898 (p90) cc_final: 0.7558 (p90)
REVERT: A  514 ASP cc_start: 0.8134 (t0) cc_final: 0.7934 (m-30)
REVERT: B   21 ARG cc_start: 0.9117 (ttp80) cc_final: 0.8788 (tpp80)
REVERT: B   41 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8315 (tm-30)
REVERT: B   54 ASN cc_start: 0.8877 (p0) cc_final: 0.8216 (p0)
REVERT: B   68 ARG cc_start: 0.7660 (ttp-110) cc_final: 0.7431 (ptm160)
REVERT: B   69 PHE cc_start: 0.8660 (m-80) cc_final: 0.7933 (m-80)
REVERT: B   82 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8908 (tt)
REVERT: B   91 ASP cc_start: 0.7332 (p0) cc_final: 0.6794 (p0)
REVERT: B   95 TYR cc_start: 0.8543 (m-10) cc_final: 0.8319 (m-10)
  outliers start: 29
  outliers final: 21
  residues processed: 151
  average time/residue: 0.1424
  time to fit residues: 28.2319
Evaluate side-chains
  151 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 PHE
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   91 THR
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  337 LEU
Chi-restraints excluded: chain A residue  430 LEU
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   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 15 optimal weight:    0.0980
   chunk 35 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 34 optimal weight:    0.4980
   chunk 17 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 60 optimal weight:    0.2980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.150825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.112521 restraints weight = 7668.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.116254 restraints weight = 4031.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.118675 restraints weight = 2788.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4829  Z= 0.176
  Angle     :  0.710  11.571   6592  Z= 0.344
  Chirality :  0.042   0.129    769
  Planarity :  0.004   0.032    813
  Dihedral  :  5.036  24.035    672
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 22.47 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.34), residues: 611
  helix: -0.35 (0.27), residues: 371
  sheet: -3.01 (0.71), residues: 49
  loop : -2.10 (0.45), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.007   0.001   PHE A 341 
 TYR   0.015   0.001   TYR A  32 
 ARG   0.005   0.000   ARG B  68 

*********************** 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
  166 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 MET cc_start: 0.7857 (tpp) cc_final: 0.7507 (tpp)
REVERT: A  191 PHE cc_start: 0.9297 (t80) cc_final: 0.8988 (t80)
REVERT: A  219 ASN cc_start: 0.8470 (t0) cc_final: 0.8053 (t0)
REVERT: A  282 ILE cc_start: 0.8987 (mm) cc_final: 0.8757 (mm)
REVERT: A  383 TRP cc_start: 0.7631 (t60) cc_final: 0.7368 (t60)
REVERT: A  436 PHE cc_start: 0.7752 (p90) cc_final: 0.7455 (p90)
REVERT: B   21 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8877 (tpp80)
REVERT: B   41 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8376 (tm-30)
REVERT: B   54 ASN cc_start: 0.8877 (p0) cc_final: 0.8250 (p0)
REVERT: B   82 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8776 (tp)
REVERT: B   91 ASP cc_start: 0.7152 (p0) cc_final: 0.6686 (p0)
REVERT: B  109 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6943 (p0)
  outliers start: 26
  outliers final: 22
  residues processed: 153
  average time/residue: 0.1459
  time to fit residues: 29.2605
Evaluate side-chains
  156 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
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  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  430 LEU
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 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   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 22 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 60 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0470
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0870
   chunk 8 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
A 238 GLN
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 GLN
B  78 ASN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.152451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.113073 restraints weight = 7586.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.116913 restraints weight = 4065.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.119418 restraints weight = 2831.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4829  Z= 0.165
  Angle     :  0.701  10.124   6592  Z= 0.339
  Chirality :  0.042   0.135    769
  Planarity :  0.003   0.032    813
  Dihedral  :  4.942  29.229    672
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 24.70 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.34), residues: 611
  helix: -0.23 (0.27), residues: 374
  sheet: -3.01 (0.66), residues: 49
  loop : -2.06 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.006   0.001   PHE A 123 
 TYR   0.015   0.001   TYR A 176 
 ARG   0.004   0.000   ARG B  47 

*********************** 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
  156 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ASN cc_start: 0.8378 (t0) cc_final: 0.7954 (t0)
REVERT: A  277 LYS cc_start: 0.8907 (mttt) cc_final: 0.8704 (mttt)
REVERT: A  282 ILE cc_start: 0.8989 (mm) cc_final: 0.8724 (mm)
REVERT: A  383 TRP cc_start: 0.7693 (t60) cc_final: 0.7414 (t60)
REVERT: A  436 PHE cc_start: 0.7799 (p90) cc_final: 0.7549 (p90)
REVERT: B   54 ASN cc_start: 0.8927 (p0) cc_final: 0.8278 (p0)
REVERT: B   69 PHE cc_start: 0.8346 (m-80) cc_final: 0.8096 (m-10)
REVERT: B   91 ASP cc_start: 0.6444 (p0) cc_final: 0.5936 (p0)
REVERT: B  109 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6942 (p0)
  outliers start: 21
  outliers final: 18
  residues processed: 146
  average time/residue: 0.1495
  time to fit residues: 28.5389
Evaluate side-chains
  142 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
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  200 PHE
Chi-restraints excluded: chain A residue  240 HIS
Chi-restraints excluded: chain A residue  430 LEU
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 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  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 26 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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**
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 = 0.3911 r_free = 0.3911 target = 0.149911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.109085 restraints weight = 7791.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112745 restraints weight = 4195.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115164 restraints weight = 2959.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4829  Z= 0.277
  Angle     :  0.741   9.363   6592  Z= 0.364
  Chirality :  0.044   0.128    769
  Planarity :  0.003   0.029    813
  Dihedral  :  5.138  27.377    672
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 23.48 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.34), residues: 611
  helix: -0.23 (0.27), residues: 374
  sheet: -2.66 (0.69), residues: 47
  loop : -2.12 (0.45), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  55 
 HIS   0.002   0.001   HIS A 240 
 PHE   0.008   0.001   PHE A 296 
 TYR   0.019   0.001   TYR A  32 
 ARG   0.005   0.001   ARG B  68 

*********************** 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
  150 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  277 LYS cc_start: 0.8956 (mttt) cc_final: 0.8753 (mttp)
REVERT: A  282 ILE cc_start: 0.9062 (mm) cc_final: 0.8811 (mm)
REVERT: A  383 TRP cc_start: 0.7703 (t60) cc_final: 0.7407 (t60)
REVERT: A  436 PHE cc_start: 0.7787 (p90) cc_final: 0.7512 (p90)
REVERT: B   54 ASN cc_start: 0.8881 (p0) cc_final: 0.8301 (p0)
REVERT: B  109 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7026 (p0)
  outliers start: 28
  outliers final: 22
  residues processed: 137
  average time/residue: 0.1543
  time to fit residues: 27.7265
Evaluate side-chains
  140 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
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  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  430 LEU
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   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 4 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 60 optimal weight:    0.1980
   chunk 31 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 34 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 GLN
B  78 ASN
** 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 = 0.3949 r_free = 0.3949 target = 0.152849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.112475 restraints weight = 7680.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.116251 restraints weight = 4131.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.118677 restraints weight = 2899.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4829  Z= 0.189
  Angle     :  0.723   9.234   6592  Z= 0.355
  Chirality :  0.043   0.133    769
  Planarity :  0.004   0.033    813
  Dihedral  :  4.998  27.375    672
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 24.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.34), residues: 611
  helix: -0.11 (0.27), residues: 372
  sheet: -2.69 (0.65), residues: 54
  loop : -2.10 (0.46), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.006   0.001   PHE A 191 
 TYR   0.018   0.001   TYR A 176 
 ARG   0.006   0.000   ARG B  68 

*********************** 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
  153 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ASN cc_start: 0.8385 (t0) cc_final: 0.7995 (t0)
REVERT: A  277 LYS cc_start: 0.8904 (mttt) cc_final: 0.8695 (mttp)
REVERT: A  282 ILE cc_start: 0.9047 (mm) cc_final: 0.8796 (mm)
REVERT: A  383 TRP cc_start: 0.7660 (t60) cc_final: 0.7387 (t60)
REVERT: A  436 PHE cc_start: 0.7730 (p90) cc_final: 0.7482 (p90)
REVERT: B   54 ASN cc_start: 0.8928 (p0) cc_final: 0.8294 (p0)
REVERT: B   95 TYR cc_start: 0.8342 (m-10) cc_final: 0.7971 (m-10)
REVERT: B  109 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6950 (p0)
  outliers start: 28
  outliers final: 24
  residues processed: 140
  average time/residue: 0.1478
  time to fit residues: 27.0937
Evaluate side-chains
  147 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
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  330 ILE
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  430 LEU
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 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 3 optimal weight:    0.0670
   chunk 48 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7920

-------------------------------------------------------------------------------
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 = 0.3942 r_free = 0.3942 target = 0.152468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.112237 restraints weight = 7608.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.116006 restraints weight = 4100.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.118440 restraints weight = 2875.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4829  Z= 0.212
  Angle     :  0.733   9.056   6592  Z= 0.361
  Chirality :  0.043   0.141    769
  Planarity :  0.004   0.059    813
  Dihedral  :  5.022  26.230    672
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 25.30 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.34), residues: 611
  helix: -0.09 (0.27), residues: 372
  sheet: -2.81 (0.60), residues: 51
  loop : -2.11 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.021   0.001   PHE B  69 
 TYR   0.017   0.001   TYR A  32 
 ARG   0.003   0.000   ARG B  47 

********************** 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
  151 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ASN cc_start: 0.8434 (t0) cc_final: 0.7971 (t0)
REVERT: A  282 ILE cc_start: 0.9045 (mm) cc_final: 0.8760 (mm)
REVERT: A  383 TRP cc_start: 0.7657 (t60) cc_final: 0.7383 (t60)
REVERT: A  436 PHE cc_start: 0.7730 (p90) cc_final: 0.7482 (p90)
REVERT: B   54 ASN cc_start: 0.8880 (p0) cc_final: 0.8245 (p0)
REVERT: B   69 PHE cc_start: 0.8458 (m-80) cc_final: 0.7719 (m-80)
REVERT: B   95 TYR cc_start: 0.8302 (m-10) cc_final: 0.7938 (m-10)
REVERT: B  109 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7076 (p0)
  outliers start: 24
  outliers final: 23
  residues processed: 140
  average time/residue: 0.1652
  time to fit residues: 29.4106
Evaluate side-chains
  145 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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  330 ILE
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  430 LEU
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
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 62.5194 > 50:
  distance: 24 - 31:  14.740
  distance: 31 - 32:  10.867
  distance: 32 - 33:  38.062
  distance: 32 - 35:  31.826
  distance: 33 - 34:  32.176
  distance: 33 - 39:  17.489
  distance: 35 - 36:  20.180
  distance: 36 - 37:  27.981
  distance: 36 - 38:  13.587
  distance: 39 - 40:  23.795
  distance: 40 - 41:  48.434
  distance: 40 - 43:  15.878
  distance: 41 - 42:  38.212
  distance: 41 - 50:  25.689
  distance: 43 - 44:  11.887
  distance: 44 - 45:  17.454
  distance: 44 - 46:  26.340
  distance: 45 - 47:  17.591
  distance: 46 - 48:  11.686
  distance: 48 - 49:  17.159
  distance: 50 - 51:   8.505
  distance: 51 - 52:  18.210
  distance: 51 - 54:  16.630
  distance: 52 - 53:  41.994
  distance: 52 - 58:  41.611
  distance: 54 - 55:  31.168
  distance: 55 - 56:  25.421
  distance: 55 - 57:   4.934
  distance: 58 - 59:  41.543
  distance: 58 - 64:  47.267
  distance: 59 - 60:  35.086
  distance: 59 - 62:  38.119
  distance: 60 - 61:  11.169
  distance: 60 - 65:  19.849
  distance: 62 - 63:  39.963
  distance: 63 - 64:  43.176
  distance: 65 - 66:  10.930
  distance: 66 - 67:  25.765
  distance: 66 - 69:  19.820
  distance: 67 - 68:  32.233
  distance: 67 - 73:  38.895
  distance: 69 - 70:  31.179
  distance: 70 - 71:  30.943
  distance: 70 - 72:  25.388
  distance: 73 - 74:  45.695
  distance: 73 - 79:  53.337
  distance: 74 - 75:  48.712
  distance: 74 - 77:  13.453
  distance: 75 - 76:  24.440
  distance: 75 - 80:  33.835
  distance: 77 - 78:  36.803
  distance: 78 - 79:  17.499
  distance: 80 - 81:  15.078
  distance: 81 - 82:  16.743
  distance: 81 - 84:  19.741
  distance: 82 - 83:  21.204
  distance: 82 - 88:  47.133
  distance: 84 - 85:  29.051
  distance: 85 - 86:  40.677
  distance: 85 - 87:  40.379
  distance: 88 - 89:  56.308
  distance: 89 - 90:  49.790
  distance: 89 - 92:  25.622
  distance: 90 - 91:  47.744
  distance: 90 - 97:  44.582
  distance: 92 - 93:  35.324
  distance: 93 - 94:  41.092
  distance: 94 - 95:  34.101
  distance: 94 - 96:  29.710
  distance: 97 - 98:  38.547
  distance: 98 - 99:  25.029
  distance: 98 - 101:  24.964
  distance: 99 - 100:  13.011
  distance: 99 - 108:   6.694
  distance: 101 - 102:  19.983
  distance: 102 - 103:   8.949
  distance: 103 - 104:  16.285
  distance: 104 - 105:  35.894
  distance: 105 - 106:  30.527
  distance: 105 - 107:  14.891
  distance: 108 - 109:   9.694
  distance: 109 - 110:   7.361
  distance: 109 - 112:  13.383
  distance: 110 - 111:  13.948
  distance: 110 - 118:  10.491
  distance: 112 - 113:  22.217
  distance: 113 - 114:  25.438
  distance: 113 - 115:  38.197
  distance: 114 - 116:  18.048
  distance: 115 - 117:  47.388
  distance: 116 - 117:  31.304