Starting phenix.real_space_refine
on Tue Mar  3 19:00:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z24_14457/03_2026/7z24_14457.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z24_14457/03_2026/7z24_14457.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z24_14457/03_2026/7z24_14457.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z24_14457/03_2026/7z24_14457.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z24_14457/03_2026/7z24_14457.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z24_14457/03_2026/7z24_14457.map"
  }
  resolution = 3.32
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      35      5.49       5
     S      13      5.16       5
     C    5266      2.51       5
     N    1378      2.21       5
     O    1611      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8303
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4260
          Classifications: {'peptide': 527}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 490}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 3303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3303
          Classifications: {'peptide': 402}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 30, 'TRANS': 371}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "E"
      Number of atoms: 720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 720
          Classifications: {'DNA': 34, 'RNA': 2}
          Modifications used: {'5*END': 1, 'rna3p': 2}
          Link IDs: {'rna3p': 35}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'NVP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.94, per 1000 atoms: 0.23
  Number of scatterers: 8303
  At special positions: 0
  Unit cell: (97, 109.61, 101.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      13     16.00
     P      35     15.00
     O    1611      8.00
     N    1378      7.00
     C    5266      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 222.7 milliseconds
  

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1750

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 11 sheets defined
      39.8% alpha, 15.7% beta
      13 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 45
      removed outlier: 3.931A  pdb=" N   VAL A  35 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   GLU A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   ILE A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 84
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 4.340A  pdb=" N   LYS A 126 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 194 through 212
      removed outlier: 3.580A  pdb=" N   THR A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TRP A 212 " --> pdb=" O   HIS A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
    Processing helix  chain 'A' and resid 253 through 268
    Processing helix  chain 'A' and resid 276 through 282
      removed outlier: 3.917A  pdb=" N   LEU A 282 " --> pdb=" O   GLN A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 4.529A  pdb=" N   GLU A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 384
    Processing helix  chain 'A' and resid 394 through 405
    Processing helix  chain 'A' and resid 473 through 488
      removed outlier: 4.006A  pdb=" N   ILE A 482 " --> pdb=" O   GLU A 478 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   TYR A 483 " --> pdb=" O   LEU A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 508
      removed outlier: 3.891A  pdb=" N   ALA A 508 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
      removed outlier: 3.602A  pdb=" N   LYS A 527 " --> pdb=" O   GLU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 546
      removed outlier: 3.576A  pdb=" N   GLU A 546 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 44
      removed outlier: 3.528A  pdb=" N   LEU B  34 " --> pdb=" O   LYS B  30 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS B  43 " --> pdb=" O   THR B  39 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU B  44 " --> pdb=" O   GLU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 85
    Processing helix  chain 'B' and resid 85 through 90
    Processing helix  chain 'B' and resid 98 through 102
      removed outlier: 3.650A  pdb=" N   LYS B 101 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 3.823A  pdb=" N   SER B 117 " --> pdb=" O   ALA B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 129
      removed outlier: 3.853A  pdb=" N   ALA B 129 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 155 through 160
    Processing helix  chain 'B' and resid 160 through 173
      Proline residue:  B 170  - end of helix
    Processing helix  chain 'B' and resid 194 through 212
      removed outlier: 3.524A  pdb=" N   THR B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 271
      removed outlier: 4.251A  pdb=" N   GLN B 269 " --> pdb=" O   ASN B 265 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE B 270 " --> pdb=" O   TRP B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 312
      removed outlier: 3.765A  pdb=" N   GLU B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS B 311 " --> pdb=" O   ARG B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 384
    Processing helix  chain 'B' and resid 394 through 402
    Processing helix  chain 'B' and resid 403 through 405
      No H-bonds generated for 'chain 'B' and resid 403 through 405'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50
      removed outlier: 4.605A  pdb=" N   ARG A 143 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110
    Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229
      removed outlier: 3.720A  pdb=" N   LYS A 238 " --> pdb=" O   HIS A 235 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 354
      removed outlier: 6.628A  pdb=" N   ILE A 341 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   THR A 351 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS A 353 " --> pdb=" O   TRP A 337 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   TRP A 337 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   GLN A 336 " --> pdb=" O   GLN A 332 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS A 390 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A 329 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362
      removed outlier: 3.528A  pdb=" N   THR A 362 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A 512 " --> pdb=" O   THR A 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 470
      removed outlier: 3.531A  pdb=" N   LYS A 465 " --> pdb=" O   TYR A 457 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU A 452 " --> pdb=" O   ASN A 447 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   TYR A 441 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLU A 438 " --> pdb=" O   ASN A 494 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   VAL A 496 " --> pdb=" O   GLU A 438 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   PHE A 440 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 63
    Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183
    Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 132
    Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253
      removed outlier: 4.239A  pdb=" N   TRP B 252 " --> pdb=" O   ILE B 293 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 355
      removed outlier: 8.868A  pdb=" N   ASN B 348 " --> pdb=" O   GLN B 343 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   GLN B 343 " --> pdb=" O   ASN B 348 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   GLN B 336 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B 329 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   PHE B 389 " --> pdb=" O   GLU B 415 " (cutoff:3.500A)

    310 hydrogen bonds defined for protein.
    840 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      36 hydrogen bonds
      72 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 0.81 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.33: 1472
        1.33 -     1.45: 2307
        1.45 -     1.57: 4721
        1.57 -     1.69: 71
        1.69 -     1.81: 23
  Bond restraints: 8594
  Sorted by residual:
  bond pdb=" N   GLU B 169 "
       pdb=" CA  GLU B 169 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.040 1.04e-02 9.25e+03 1.51e+01
  bond pdb=" N   VAL B 241 "
       pdb=" CA  VAL B 241 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.045 1.19e-02 7.06e+03 1.40e+01
  bond pdb=" N   ILE B 293 "
       pdb=" CA  ILE B 293 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 8.70e-03 1.32e+04 1.35e+01
  bond pdb=" N   ILE B 244 "
       pdb=" CA  ILE B 244 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.044 1.22e-02 6.72e+03 1.29e+01
  bond pdb=" N   GLY B 285 "
       pdb=" CA  GLY B 285 "
    ideal  model  delta    sigma   weight residual
    1.444  1.478 -0.035 1.02e-02 9.61e+03 1.15e+01
  ... (remaining 8589 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 11443
        2.75 -     5.51: 357
        5.51 -     8.26: 29
        8.26 -    11.02: 3
       11.02 -    13.77: 2
  Bond angle restraints: 11834
  Sorted by residual:
  angle pdb=" C5'  DG E  12 "
        pdb=" C4'  DG E  12 "
        pdb=" O4'  DG E  12 "
      ideal   model   delta    sigma   weight residual
     109.40  123.17  -13.77 1.50e+00 4.44e-01 8.43e+01
  angle pdb=" C5'  DT E  13 "
        pdb=" C4'  DT E  13 "
        pdb=" O4'  DT E  13 "
      ideal   model   delta    sigma   weight residual
     109.40  122.69  -13.29 1.50e+00 4.44e-01 7.85e+01
  angle pdb=" C5'  DG E  19 "
        pdb=" C4'  DG E  19 "
        pdb=" O4'  DG E  19 "
      ideal   model   delta    sigma   weight residual
     109.40  120.19  -10.79 1.50e+00 4.44e-01 5.17e+01
  angle pdb=" C   HIS B 235 "
        pdb=" CA  HIS B 235 "
        pdb=" CB  HIS B 235 "
      ideal   model   delta    sigma   weight residual
     110.08  117.91   -7.83 1.15e+00 7.56e-01 4.63e+01
  angle pdb=" C3' OMC E   2 "
        pdb=" C2' OMC E   2 "
        pdb=" C1' OMC E   2 "
      ideal   model   delta    sigma   weight residual
     101.30  106.98   -5.68 1.00e+00 1.00e+00 3.22e+01
  ... (remaining 11829 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.40: 4354
       19.40 -    38.80: 495
       38.80 -    58.20: 137
       58.20 -    77.59: 31
       77.59 -    96.99: 8
  Dihedral angle restraints: 5025
    sinusoidal: 2313
      harmonic: 2712
  Sorted by residual:
  dihedral pdb=" C   PHE B 346 "
           pdb=" N   PHE B 346 "
           pdb=" CA  PHE B 346 "
           pdb=" CB  PHE B 346 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.18   10.58     0      2.50e+00 1.60e-01 1.79e+01
  dihedral pdb=" C   GLU B 291 "
           pdb=" N   GLU B 291 "
           pdb=" CA  GLU B 291 "
           pdb=" CB  GLU B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.67   10.07     0      2.50e+00 1.60e-01 1.62e+01
  dihedral pdb=" CD  ARG A 277 "
           pdb=" NE  ARG A 277 "
           pdb=" CZ  ARG A 277 "
           pdb=" NH1 ARG A 277 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   32.46  -32.46     1      1.00e+01 1.00e-02 1.50e+01
  ... (remaining 5022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 1140
       0.109 -    0.217: 125
       0.217 -    0.326: 23
       0.326 -    0.434: 2
       0.434 -    0.543: 2
  Chirality restraints: 1292
  Sorted by residual:
  chirality pdb=" C4'  DG E  12 "
            pdb=" C5'  DG E  12 "
            pdb=" O4'  DG E  12 "
            pdb=" C3'  DG E  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -1.98   -0.54 2.00e-01 2.50e+01 7.36e+00
  chirality pdb=" C4'  DT E  13 "
            pdb=" C5'  DT E  13 "
            pdb=" O4'  DT E  13 "
            pdb=" C3'  DT E  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.07   -0.45 2.00e-01 2.50e+01 5.09e+00
  chirality pdb=" C4'  DC E  20 "
            pdb=" C5'  DC E  20 "
            pdb=" O4'  DC E  20 "
            pdb=" C3'  DC E  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.17   -0.36 2.00e-01 2.50e+01 3.16e+00
  ... (remaining 1289 not shown)

  Planarity restraints: 1367
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 277 "    0.582 9.50e-02 1.11e+02   2.61e-01 4.16e+01
        pdb=" NE  ARG A 277 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 277 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 277 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 277 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 419 "    0.079 5.00e-02 4.00e+02   1.17e-01 2.20e+01
        pdb=" N   PRO B 420 "   -0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO B 420 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO B 420 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 246 "   -0.057 5.00e-02 4.00e+02   8.69e-02 1.21e+01
        pdb=" N   PRO A 247 "    0.150 5.00e-02 4.00e+02
        pdb=" CA  PRO A 247 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 247 "   -0.047 5.00e-02 4.00e+02
  ... (remaining 1364 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 3009
        2.89 -     3.39: 7440
        3.39 -     3.89: 13877
        3.89 -     4.40: 15907
        4.40 -     4.90: 26057
  Nonbonded interactions: 66290
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 276 "
            pdb=" OG  SER A 280 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" OG1 THR A 286 "
            pdb=" OE2 GLU A 291 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" O   TYR B  56 "
            pdb=" NH2 ARG B 143 "
     model   vdw
     2.417 3.120
  nonbonded pdb=" N   THR B 290 "
            pdb=" OG1 THR B 290 "
     model   vdw
     2.459 2.496
  nonbonded pdb=" OE1 GLN A 330 "
            pdb=" NE2 GLN A 340 "
     model   vdw
     2.466 3.120
  ... (remaining 66285 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 individual isotropic
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:             0.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.280
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
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      :  0.007   0.087   8594  Z= 0.468
  Angle     :  1.050  13.772  11834  Z= 0.706
  Chirality :  0.076   0.543   1292
  Planarity :  0.010   0.261   1367
  Dihedral  : 18.098  96.992   3275
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  3.04 %
    Favored  : 94.89 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.28), residues: 917
  helix:  1.09 (0.30), residues: 311
  sheet: -0.29 (0.40), residues: 177
  loop : -0.90 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 211 
 TYR   0.020   0.002   TYR A 532 
 PHE   0.021   0.002   PHE A 124 
 TRP   0.043   0.002   TRP B 414 
 HIS   0.006   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00728 ( 8594)
  covalent geometry    : angle       1.05008 (11834)
  hydrogen bonds       : bond        0.17674 (  346)
  hydrogen bonds       : angle       7.54200 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  498 ASN cc_start: 0.6968 (t0) cc_final: 0.6588 (t0)
REVERT: B  280 SER cc_start: 0.7756 (p) cc_final: 0.7080 (t)
  outliers start: 17
  outliers final: 9
  residues processed: 134
  average time/residue: 0.0842
  time to fit residues: 15.8103
Evaluate side-chains
  105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
A 255 ASN
A 332 GLN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.214690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.175299 restraints weight = 8665.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 1.97
r_work: 0.3668 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.1037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8594  Z= 0.155
  Angle     :  0.605   7.300  11834  Z= 0.320
  Chirality :  0.042   0.144   1292
  Planarity :  0.006   0.078   1367
  Dihedral  : 16.960  81.910   1360
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  9.73 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.28), residues: 917
  helix:  1.02 (0.29), residues: 331
  sheet: -0.17 (0.39), residues: 172
  loop : -0.89 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  83 
 TYR   0.012   0.002   TYR A 501 
 PHE   0.017   0.001   PHE B  87 
 TRP   0.018   0.002   TRP B 414 
 HIS   0.004   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8594)
  covalent geometry    : angle       0.60520 (11834)
  hydrogen bonds       : bond        0.04396 (  346)
  hydrogen bonds       : angle       5.10416 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.4779 (mt) cc_final: 0.4538 (mp)
REVERT: A   78 ARG cc_start: 0.6123 (mmp80) cc_final: 0.5328 (mmt-90)
REVERT: A  147 ASN cc_start: 0.7235 (m110) cc_final: 0.6696 (t0)
REVERT: A  375 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8127 (mt)
REVERT: A  530 LYS cc_start: 0.7023 (mtpt) cc_final: 0.6761 (mtmt)
REVERT: B  233 GLU cc_start: 0.6497 (mp0) cc_final: 0.6116 (pt0)
REVERT: B  280 SER cc_start: 0.7766 (p) cc_final: 0.7314 (t)
  outliers start: 16
  outliers final: 12
  residues processed: 116
  average time/residue: 0.0849
  time to fit residues: 13.7995
Evaluate side-chains
  109 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   chunk 43 optimal weight:    8.9990
   chunk 86 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 73 optimal weight:   20.0000
   chunk 42 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   overall best weight:    5.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
A 332 GLN
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 545 ASN ** 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 = 0.4321 r_free = 0.4321 target = 0.211805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.172163 restraints weight = 8644.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 1.95
r_work: 0.3677 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8594  Z= 0.210
  Angle     :  0.648  10.453  11834  Z= 0.339
  Chirality :  0.044   0.144   1292
  Planarity :  0.006   0.066   1367
  Dihedral  : 16.863  82.286   1356
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.41 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.27), residues: 917
  helix:  0.76 (0.29), residues: 333
  sheet: -0.02 (0.41), residues: 154
  loop : -1.00 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  78 
 TYR   0.016   0.002   TYR A 501 
 PHE   0.025   0.002   PHE B  87 
 TRP   0.017   0.002   TRP B 402 
 HIS   0.007   0.002   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 8594)
  covalent geometry    : angle       0.64785 (11834)
  hydrogen bonds       : bond        0.04502 (  346)
  hydrogen bonds       : angle       5.02243 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  147 ASN cc_start: 0.7264 (m110) cc_final: 0.6772 (t0)
REVERT: A  375 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8155 (mt)
REVERT: A  530 LYS cc_start: 0.7115 (mtpt) cc_final: 0.6856 (mtmt)
REVERT: B  101 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.5692 (mttm)
REVERT: B  233 GLU cc_start: 0.6618 (mp0) cc_final: 0.6380 (pm20)
REVERT: B  280 SER cc_start: 0.7884 (p) cc_final: 0.7363 (t)
  outliers start: 23
  outliers final: 16
  residues processed: 117
  average time/residue: 0.0848
  time to fit residues: 13.8892
Evaluate side-chains
  115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  239 TRP
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    0.5980
   chunk 75 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 175 ASN
A 336 GLN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.217689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.178500 restraints weight = 8788.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 1.92
r_work: 0.3710 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8594  Z= 0.113
  Angle     :  0.526   7.830  11834  Z= 0.276
  Chirality :  0.040   0.140   1292
  Planarity :  0.005   0.055   1367
  Dihedral  : 16.509  81.248   1355
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.48 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.28), residues: 917
  helix:  1.25 (0.30), residues: 332
  sheet: -0.24 (0.39), residues: 178
  loop : -0.65 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  83 
 TYR   0.012   0.001   TYR A 501 
 PHE   0.021   0.001   PHE B  87 
 TRP   0.018   0.001   TRP B 402 
 HIS   0.002   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8594)
  covalent geometry    : angle       0.52566 (11834)
  hydrogen bonds       : bond        0.02954 (  346)
  hydrogen bonds       : angle       4.58289 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   29 GLU cc_start: 0.4978 (OUTLIER) cc_final: 0.4755 (tp30)
REVERT: A   34 LEU cc_start: 0.4552 (OUTLIER) cc_final: 0.4344 (tt)
REVERT: A  147 ASN cc_start: 0.7277 (m110) cc_final: 0.6793 (t0)
REVERT: A  375 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8119 (mt)
REVERT: A  530 LYS cc_start: 0.6923 (mtpt) cc_final: 0.6682 (mtmt)
REVERT: B  206 ARG cc_start: 0.7121 (ttp80) cc_final: 0.6409 (ttp-170)
REVERT: B  233 GLU cc_start: 0.6512 (mp0) cc_final: 0.6272 (pm20)
REVERT: B  280 SER cc_start: 0.7769 (p) cc_final: 0.7209 (t)
  outliers start: 16
  outliers final: 9
  residues processed: 123
  average time/residue: 0.0841
  time to fit residues: 14.5991
Evaluate side-chains
  113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 74 optimal weight:    0.0170
   chunk 59 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9990
   chunk 79 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9980
   chunk 23 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    1.4024

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

Flipped N/Q/H residues before XYZ refinement:
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.218766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.177578 restraints weight = 8687.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 2.00
r_work: 0.3753 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8594  Z= 0.114
  Angle     :  0.523   8.555  11834  Z= 0.272
  Chirality :  0.040   0.168   1292
  Planarity :  0.005   0.050   1367
  Dihedral  : 16.425  81.338   1351
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.84 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.28), residues: 917
  helix:  1.37 (0.30), residues: 331
  sheet: -0.16 (0.39), residues: 178
  loop : -0.58 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  83 
 TYR   0.017   0.001   TYR A 501 
 PHE   0.023   0.001   PHE B  87 
 TRP   0.014   0.001   TRP B 402 
 HIS   0.002   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8594)
  covalent geometry    : angle       0.52307 (11834)
  hydrogen bonds       : bond        0.02962 (  346)
  hydrogen bonds       : angle       4.51920 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.4329 (OUTLIER) cc_final: 0.4092 (tt)
REVERT: A  147 ASN cc_start: 0.7287 (m110) cc_final: 0.6747 (t0)
REVERT: A  375 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8032 (mt)
REVERT: A  530 LYS cc_start: 0.6818 (mtpt) cc_final: 0.6588 (mtmt)
REVERT: B  233 GLU cc_start: 0.6573 (mp0) cc_final: 0.6354 (pm20)
REVERT: B  280 SER cc_start: 0.7930 (p) cc_final: 0.7382 (t)
  outliers start: 17
  outliers final: 13
  residues processed: 116
  average time/residue: 0.0855
  time to fit residues: 13.9876
Evaluate side-chains
  117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 3 optimal weight:   40.0000
   chunk 41 optimal weight:    7.9990
   chunk 92 optimal weight:   20.0000
   chunk 84 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0020
   chunk 46 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 26 optimal weight:   30.0000
   overall best weight:    3.7194

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
A 428 GLN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 545 ASN ** 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 = 0.4345 r_free = 0.4345 target = 0.215039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.174027 restraints weight = 8635.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.12
r_work: 0.3664 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8594  Z= 0.158
  Angle     :  0.574  10.403  11834  Z= 0.296
  Chirality :  0.042   0.191   1292
  Planarity :  0.005   0.049   1367
  Dihedral  : 16.671  82.015   1351
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.60 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.28), residues: 917
  helix:  1.16 (0.29), residues: 331
  sheet: -0.06 (0.39), residues: 164
  loop : -0.61 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  83 
 TYR   0.033   0.002   TYR A 319 
 PHE   0.023   0.002   PHE B  87 
 TRP   0.014   0.001   TRP A 402 
 HIS   0.006   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8594)
  covalent geometry    : angle       0.57373 (11834)
  hydrogen bonds       : bond        0.03563 (  346)
  hydrogen bonds       : angle       4.63961 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.4338 (OUTLIER) cc_final: 0.4112 (tt)
REVERT: A  147 ASN cc_start: 0.7253 (m110) cc_final: 0.6719 (t0)
REVERT: A  375 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8174 (mt)
REVERT: A  530 LYS cc_start: 0.6923 (mtpt) cc_final: 0.6712 (mtpt)
REVERT: B  206 ARG cc_start: 0.7202 (ttp80) cc_final: 0.6469 (ttp-170)
REVERT: B  233 GLU cc_start: 0.6556 (mp0) cc_final: 0.6336 (pm20)
REVERT: B  280 SER cc_start: 0.7994 (p) cc_final: 0.7440 (t)
  outliers start: 21
  outliers final: 17
  residues processed: 114
  average time/residue: 0.0920
  time to fit residues: 14.7534
Evaluate side-chains
  117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 75 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   chunk 20 optimal weight:    0.0070
   chunk 80 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    2.2006

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

Flipped N/Q/H residues before XYZ refinement:
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.217515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.176635 restraints weight = 8687.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.12
r_work: 0.3659 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8594  Z= 0.124
  Angle     :  0.543   9.705  11834  Z= 0.281
  Chirality :  0.041   0.173   1292
  Planarity :  0.005   0.045   1367
  Dihedral  : 16.615  81.385   1351
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.33 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.28), residues: 917
  helix:  1.31 (0.30), residues: 331
  sheet: -0.17 (0.39), residues: 175
  loop : -0.57 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  83 
 TYR   0.025   0.001   TYR A 319 
 PHE   0.022   0.001   PHE B  87 
 TRP   0.017   0.001   TRP A 402 
 HIS   0.004   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8594)
  covalent geometry    : angle       0.54301 (11834)
  hydrogen bonds       : bond        0.03107 (  346)
  hydrogen bonds       : angle       4.56949 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.4298 (OUTLIER) cc_final: 0.4071 (tt)
REVERT: A  147 ASN cc_start: 0.7255 (m110) cc_final: 0.6688 (t0)
REVERT: A  375 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8124 (mt)
REVERT: A  530 LYS cc_start: 0.6865 (mtpt) cc_final: 0.6652 (mtmt)
REVERT: B  206 ARG cc_start: 0.7173 (ttp80) cc_final: 0.6462 (ttp-170)
REVERT: B  233 GLU cc_start: 0.6558 (mp0) cc_final: 0.6314 (pm20)
REVERT: B  280 SER cc_start: 0.7988 (p) cc_final: 0.7428 (t)
  outliers start: 18
  outliers final: 14
  residues processed: 117
  average time/residue: 0.0836
  time to fit residues: 14.0959
Evaluate side-chains
  118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 27 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.214891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.173593 restraints weight = 8659.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 2.13
r_work: 0.3690 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8594  Z= 0.156
  Angle     :  0.576  11.345  11834  Z= 0.297
  Chirality :  0.042   0.170   1292
  Planarity :  0.005   0.045   1367
  Dihedral  : 16.669  81.526   1351
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.84 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.28), residues: 917
  helix:  1.17 (0.29), residues: 333
  sheet: -0.32 (0.38), residues: 180
  loop : -0.67 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  83 
 TYR   0.025   0.002   TYR A 319 
 PHE   0.025   0.002   PHE B  87 
 TRP   0.015   0.002   TRP A 402 
 HIS   0.005   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8594)
  covalent geometry    : angle       0.57593 (11834)
  hydrogen bonds       : bond        0.03500 (  346)
  hydrogen bonds       : angle       4.67232 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.4108 (tt)
REVERT: A   83 ARG cc_start: 0.7189 (mmp80) cc_final: 0.6418 (mmp80)
REVERT: A  375 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8183 (mt)
REVERT: A  530 LYS cc_start: 0.6976 (mtpt) cc_final: 0.6776 (mtpt)
REVERT: B  206 ARG cc_start: 0.7124 (ttp80) cc_final: 0.6458 (ttp-170)
REVERT: B  233 GLU cc_start: 0.6645 (mp0) cc_final: 0.6392 (pm20)
REVERT: B  280 SER cc_start: 0.8019 (p) cc_final: 0.7453 (t)
  outliers start: 23
  outliers final: 19
  residues processed: 114
  average time/residue: 0.0900
  time to fit residues: 14.3858
Evaluate side-chains
  118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  377 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 23 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 19 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.216464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.174913 restraints weight = 8719.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 2.18
r_work: 0.3648 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8594  Z= 0.126
  Angle     :  0.546  10.833  11834  Z= 0.281
  Chirality :  0.041   0.169   1292
  Planarity :  0.005   0.045   1367
  Dihedral  : 16.535  81.057   1351
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.69 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.28), residues: 917
  helix:  1.30 (0.30), residues: 331
  sheet: -0.12 (0.39), residues: 174
  loop : -0.53 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  83 
 TYR   0.023   0.002   TYR A 319 
 PHE   0.026   0.001   PHE B  87 
 TRP   0.018   0.001   TRP A 402 
 HIS   0.004   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8594)
  covalent geometry    : angle       0.54647 (11834)
  hydrogen bonds       : bond        0.03127 (  346)
  hydrogen bonds       : angle       4.55857 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.4312 (OUTLIER) cc_final: 0.4071 (tt)
REVERT: A   83 ARG cc_start: 0.7167 (mmp80) cc_final: 0.6406 (mmp80)
REVERT: A  375 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8103 (mt)
REVERT: A  530 LYS cc_start: 0.6945 (mtpt) cc_final: 0.6731 (mtmt)
REVERT: B  206 ARG cc_start: 0.7057 (ttp80) cc_final: 0.6413 (ttp-170)
REVERT: B  233 GLU cc_start: 0.6627 (mp0) cc_final: 0.6412 (pm20)
REVERT: B  280 SER cc_start: 0.7999 (p) cc_final: 0.7429 (t)
  outliers start: 17
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0847
  time to fit residues: 13.4188
Evaluate side-chains
  112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 19 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:   20.0000
   chunk 84 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.217961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.176370 restraints weight = 8671.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 2.08
r_work: 0.3714 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8594  Z= 0.115
  Angle     :  0.527   9.990  11834  Z= 0.271
  Chirality :  0.040   0.168   1292
  Planarity :  0.005   0.044   1367
  Dihedral  : 16.417  80.923   1351
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.82 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.28), residues: 917
  helix:  1.45 (0.30), residues: 329
  sheet: -0.19 (0.39), residues: 179
  loop : -0.49 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  83 
 TYR   0.036   0.001   TYR A 319 
 PHE   0.026   0.001   PHE B  87 
 TRP   0.021   0.001   TRP A 402 
 HIS   0.003   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8594)
  covalent geometry    : angle       0.52674 (11834)
  hydrogen bonds       : bond        0.02929 (  346)
  hydrogen bonds       : angle       4.46942 (  912)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A   34 LEU cc_start: 0.4241 (OUTLIER) cc_final: 0.3980 (tt)
REVERT: A   83 ARG cc_start: 0.7195 (mmp80) cc_final: 0.6401 (mmp80)
REVERT: A  358 ARG cc_start: 0.6518 (mtp180) cc_final: 0.6307 (ptp-170)
REVERT: A  375 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8117 (mt)
REVERT: B  206 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6384 (ttp-170)
REVERT: B  233 GLU cc_start: 0.6702 (mp0) cc_final: 0.6362 (tt0)
REVERT: B  280 SER cc_start: 0.7996 (p) cc_final: 0.7435 (t)
  outliers start: 18
  outliers final: 14
  residues processed: 116
  average time/residue: 0.0821
  time to fit residues: 13.4563
Evaluate side-chains
  113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  317 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 38 optimal weight:    0.0570
   chunk 54 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 23 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 84 optimal weight:    0.0670
   chunk 73 optimal weight:   10.0000
   chunk 94 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 60 optimal weight:   20.0000
   chunk 76 optimal weight:    6.9990
   overall best weight:    3.4242

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

Flipped N/Q/H residues before XYZ refinement:
A 336 GLN
** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.215934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.173882 restraints weight = 8663.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 2.08
r_work: 0.3689 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8594  Z= 0.148
  Angle     :  0.563  11.242  11834  Z= 0.290
  Chirality :  0.042   0.170   1292
  Planarity :  0.005   0.045   1367
  Dihedral  : 16.511  81.229   1351
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.94 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.28), residues: 917
  helix:  1.29 (0.29), residues: 331
  sheet: -0.34 (0.38), residues: 179
  loop : -0.54 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  83 
 TYR   0.039   0.002   TYR A 319 
 PHE   0.027   0.002   PHE B  87 
 TRP   0.022   0.002   TRP B 410 
 HIS   0.005   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8594)
  covalent geometry    : angle       0.56297 (11834)
  hydrogen bonds       : bond        0.03351 (  346)
  hydrogen bonds       : angle       4.59500 (  912)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1779.61 seconds
wall clock time: 31 minutes 15.99 seconds (1875.99 seconds total)