Starting phenix.real_space_refine
on Tue Nov 18 02:29:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xhb_33193/11_2025/7xhb_33193.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xhb_33193/11_2025/7xhb_33193.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xhb_33193/11_2025/7xhb_33193.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xhb_33193/11_2025/7xhb_33193.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xhb_33193/11_2025/7xhb_33193.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xhb_33193/11_2025/7xhb_33193.map"
  }
  resolution = 3.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.061
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      46      5.16       5
     C    6473      2.51       5
     N    1727      2.21       5
     O    1873      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10122
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 765, 6107
          Classifications: {'peptide': 765}
          Link IDs: {'PTRANS': 15, 'TRANS': 749}
    Chain: "Y"
      Number of atoms: 3198
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 407, 3194
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 20, 'TRANS': 386}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 407, 3194
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 20, 'TRANS': 386}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 3261
    Chain: "E"
      Number of atoms: 480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 480
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 1, 'TRANS': 56}
    Chain: "B"
      Number of atoms: 309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 309
          Classifications: {'peptide': 42}
          Link IDs: {'TRANS': 41}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLY Y 145 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY Y 145 " occ=0.50
  Time building chain proxies: 2.69, per 1000 atoms: 0.27
  Number of scatterers: 10122
  At special positions: 0
  Unit cell: (98.115, 119.215, 128.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      46     16.00
     P       2     15.00
     Mg      1     11.99
     O    1873      8.00
     N    1727      7.00
     C    6473      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: 0.95
  Conformation dependent library (CDL) restraints added in 502.8 milliseconds
  

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2366

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      65.2% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 33
    Processing helix  chain 'A' and resid 37 through 54
    Processing helix  chain 'A' and resid 61 through 78
    Processing helix  chain 'A' and resid 82 through 94
    Processing helix  chain 'A' and resid 106 through 119
      removed outlier: 4.883A  pdb=" N   LEU A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      Proline residue:  A 113  - end of helix
    Processing helix  chain 'A' and resid 130 through 146
      removed outlier: 4.813A  pdb=" N   ILE A 144 " --> pdb=" O   GLN A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 169
    Processing helix  chain 'A' and resid 177 through 188
    Processing helix  chain 'A' and resid 208 through 213
    Processing helix  chain 'A' and resid 231 through 242
    Processing helix  chain 'A' and resid 262 through 273
    Processing helix  chain 'A' and resid 283 through 297
    Processing helix  chain 'A' and resid 301 through 305
    Processing helix  chain 'A' and resid 333 through 341
    Processing helix  chain 'A' and resid 356 through 363
    Processing helix  chain 'A' and resid 375 through 385
      removed outlier: 4.457A  pdb=" N   ASN A 383 " --> pdb=" O   GLU A 379 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 384 " --> pdb=" O   GLU A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 429
      removed outlier: 3.941A  pdb=" N   THR A 428 " --> pdb=" O   GLN A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 452
      removed outlier: 3.747A  pdb=" N   SER A 442 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 465
      No H-bonds generated for 'chain 'A' and resid 463 through 465'
    Processing helix  chain 'A' and resid 466 through 474
    Processing helix  chain 'A' and resid 515 through 524
      removed outlier: 4.005A  pdb=" N   ASP A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 549
    Processing helix  chain 'A' and resid 551 through 559
      removed outlier: 3.845A  pdb=" N   MET A 555 " --> pdb=" O   ALA A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 620
      removed outlier: 3.889A  pdb=" N   GLN A 598 " --> pdb=" O   LYS A 594 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   VAL A 602 " --> pdb=" O   GLN A 598 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   LEU A 603 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 643
    Processing helix  chain 'A' and resid 653 through 665
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.694A  pdb=" N   ILE A 676 " --> pdb=" O   LYS A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 701
    Processing helix  chain 'A' and resid 705 through 738
      removed outlier: 3.691A  pdb=" N   ARG A 709 " --> pdb=" O   LYS A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 745
      removed outlier: 3.828A  pdb=" N   ALA A 742 " --> pdb=" O   HIS A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 777
      removed outlier: 3.687A  pdb=" N   PHE A 757 " --> pdb=" O   GLN A 753 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 3 through 10
    Processing helix  chain 'Y' and resid 11 through 34
      removed outlier: 3.731A  pdb=" N   ILE Y  34 " --> pdb=" O   ILE Y  30 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 40 through 48
      removed outlier: 3.646A  pdb=" N   ASP Y  48 " --> pdb=" O   LEU Y  44 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 74 through 87
    Processing helix  chain 'Y' and resid 92 through 101
    Processing helix  chain 'Y' and resid 103 through 136
      removed outlier: 3.749A  pdb=" N   LEU Y 126 " --> pdb=" O   PHE Y 122 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 148 through 173
      removed outlier: 3.554A  pdb=" N   ALA Y 172 " --> pdb=" O   GLU Y 168 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 177 through 189
      removed outlier: 3.507A  pdb=" N   ILE Y 182 " --> pdb=" O   GLY Y 178 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 190 through 203
      removed outlier: 4.341A  pdb=" N   TYR Y 199 " --> pdb=" O   LEU Y 195 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA Y 200 " --> pdb=" O   ASN Y 196 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   PHE Y 203 " --> pdb=" O   TYR Y 199 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 214 through 236
    Processing helix  chain 'Y' and resid 271 through 283
    Processing helix  chain 'Y' and resid 283 through 288
      removed outlier: 4.071A  pdb=" N   ILE Y 287 " --> pdb=" O   ALA Y 283 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 294 through 304
    Processing helix  chain 'Y' and resid 308 through 331
      removed outlier: 4.130A  pdb=" N   ILE Y 314 " --> pdb=" O   VAL Y 310 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 332 through 343
      removed outlier: 3.684A  pdb=" N   GLN Y 343 " --> pdb=" O   ASN Y 339 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 354 through 381
      removed outlier: 3.958A  pdb=" N   LEU Y 369 " --> pdb=" O   TYR Y 365 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   VAL Y 370 " --> pdb=" O   ARG Y 366 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 382 through 387
      removed outlier: 3.583A  pdb=" N   ASN Y 387 " --> pdb=" O   VAL Y 383 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 399 through 417
      removed outlier: 4.402A  pdb=" N   VAL Y 405 " --> pdb=" O   SER Y 401 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   MET Y 413 " --> pdb=" O   ALA Y 409 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 419 through 424
      removed outlier: 3.716A  pdb=" N   HIS Y 424 " --> pdb=" O   LEU Y 420 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 15
    Processing helix  chain 'E' and resid 16 through 18
      No H-bonds generated for 'chain 'E' and resid 16 through 18'
    Processing helix  chain 'E' and resid 22 through 59
    Processing helix  chain 'B' and resid 3 through 21
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 99
      removed outlier: 6.723A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 176
      removed outlier: 6.651A  pdb=" N   VAL A 124 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   SER A 175 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   VAL A 126 " --> pdb=" O   SER A 175 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   GLY A 123 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE A 203 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL A 205 " --> pdb=" O   HIS A 125 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   HIS A 202 " --> pdb=" O   LYS A 366 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 329
      removed outlier: 3.780A  pdb=" N   ALA A 353 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   GLY A 225 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   THR A 351 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 251
    Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 308
      removed outlier: 3.766A  pdb=" N   ILE A 315 " --> pdb=" O   MET A 324 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402
      removed outlier: 3.938A  pdb=" N   ILE A 534 " --> pdb=" O   LEU A 505 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   VAL A 432 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   ALA A 483 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   VAL A 434 " --> pdb=" O   ALA A 483 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 406 through 407
      removed outlier: 3.581A  pdb=" N   ILE A 569 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'Y' and resid 238 through 241

    613 hydrogen bonds defined for protein.
    1809 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: 1.71

  Time building geometry restraints manager: 1.27 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: 3081
        1.34 -     1.46: 1670
        1.46 -     1.58: 5452
        1.58 -     1.69: 3
        1.69 -     1.81: 91
  Bond restraints: 10297
  Sorted by residual:
  bond pdb=" CA  GLN Y 396 "
       pdb=" CB  GLN Y 396 "
    ideal  model  delta    sigma   weight residual
    1.527  1.575 -0.048 1.75e-02 3.27e+03 7.59e+00
  bond pdb=" CB  ASP Y  48 "
       pdb=" CG  ASP Y  48 "
    ideal  model  delta    sigma   weight residual
    1.516  1.568 -0.052 2.50e-02 1.60e+03 4.31e+00
  bond pdb=" CA  THR A 410 "
       pdb=" CB  THR A 410 "
    ideal  model  delta    sigma   weight residual
    1.530  1.563 -0.033 1.69e-02 3.50e+03 3.84e+00
  bond pdb=" C   ILE Y 191 "
       pdb=" N   PRO Y 192 "
    ideal  model  delta    sigma   weight residual
    1.336  1.360 -0.024 1.23e-02 6.61e+03 3.82e+00
  bond pdb=" N   PRO Y 392 "
       pdb=" CA  PRO Y 392 "
    ideal  model  delta    sigma   weight residual
    1.465  1.502 -0.037 2.03e-02 2.43e+03 3.32e+00
  ... (remaining 10292 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.88: 13726
        3.88 -     7.76: 155
        7.76 -    11.63: 24
       11.63 -    15.51: 1
       15.51 -    19.39: 1
  Bond angle restraints: 13907
  Sorted by residual:
  angle pdb=" N   LEU A 221 "
        pdb=" CA  LEU A 221 "
        pdb=" C   LEU A 221 "
      ideal   model   delta    sigma   weight residual
     108.20   88.81   19.39 1.71e+00 3.42e-01 1.29e+02
  angle pdb=" N   ILE A 222 "
        pdb=" CA  ILE A 222 "
        pdb=" C   ILE A 222 "
      ideal   model   delta    sigma   weight residual
     108.11   96.86   11.25 1.40e+00 5.10e-01 6.46e+01
  angle pdb=" N   TYR B  50 "
        pdb=" CA  TYR B  50 "
        pdb=" C   TYR B  50 "
      ideal   model   delta    sigma   weight residual
     108.73   95.68   13.05 1.63e+00 3.76e-01 6.41e+01
  angle pdb=" C   GLN Y  47 "
        pdb=" N   ASP Y  48 "
        pdb=" CA  ASP Y  48 "
      ideal   model   delta    sigma   weight residual
     125.66  136.71  -11.05 1.85e+00 2.92e-01 3.57e+01
  angle pdb=" N   ALA B  47 "
        pdb=" CA  ALA B  47 "
        pdb=" C   ALA B  47 "
      ideal   model   delta    sigma   weight residual
     108.20  118.34  -10.14 1.71e+00 3.42e-01 3.52e+01
  ... (remaining 13902 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.47: 6007
       23.47 -    46.95: 193
       46.95 -    70.42: 4
       70.42 -    93.89: 7
       93.89 -   117.37: 1
  Dihedral angle restraints: 6212
    sinusoidal: 2531
      harmonic: 3681
  Sorted by residual:
  dihedral pdb=" CA  LEU Y 391 "
           pdb=" C   LEU Y 391 "
           pdb=" N   PRO Y 392 "
           pdb=" CA  PRO Y 392 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.78  -46.22     0      5.00e+00 4.00e-02 8.54e+01
  dihedral pdb=" CA  HIS Y 308 "
           pdb=" C   HIS Y 308 "
           pdb=" N   PRO Y 309 "
           pdb=" CA  PRO Y 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.43  -31.57     0      5.00e+00 4.00e-02 3.99e+01
  dihedral pdb=" C5' ADP A1002 "
           pdb=" O5' ADP A1002 "
           pdb=" PA  ADP A1002 "
           pdb=" O2A ADP A1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -177.36  117.37     1      2.00e+01 2.50e-03 3.50e+01
  ... (remaining 6209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1227
       0.068 -    0.135: 307
       0.135 -    0.203: 38
       0.203 -    0.270: 11
       0.270 -    0.338: 4
  Chirality restraints: 1587
  Sorted by residual:
  chirality pdb=" CB  VAL Y 331 "
            pdb=" CA  VAL Y 331 "
            pdb=" CG1 VAL Y 331 "
            pdb=" CG2 VAL Y 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.85e+00
  chirality pdb=" CA  THR A 410 "
            pdb=" N   THR A 410 "
            pdb=" C   THR A 410 "
            pdb=" CB  THR A 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.22    0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CA  LEU A 221 "
            pdb=" N   LEU A 221 "
            pdb=" C   LEU A 221 "
            pdb=" CB  LEU A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.28e+00
  ... (remaining 1584 not shown)

  Planarity restraints: 1778
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO Y 284 "    0.055 5.00e-02 4.00e+02   8.18e-02 1.07e+01
        pdb=" N   PRO Y 285 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO Y 285 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO Y 285 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 241 "   -0.013 2.00e-02 2.50e+03   2.48e-02 6.16e+00
        pdb=" C   VAL A 241 "    0.043 2.00e-02 2.50e+03
        pdb=" O   VAL A 241 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ARG A 242 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 174 "    0.013 2.00e-02 2.50e+03   1.67e-02 5.61e+00
        pdb=" CG  TYR A 174 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 174 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 174 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 174 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 174 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 174 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 174 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1775 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 154
        2.67 -     3.23: 9249
        3.23 -     3.79: 15866
        3.79 -     4.34: 20654
        4.34 -     4.90: 33810
  Nonbonded interactions: 79733
  Sorted by model distance:
  nonbonded pdb="MG    MG A1001 "
            pdb=" O2B ADP A1002 "
     model   vdw
     2.115 2.170
  nonbonded pdb=" O   ILE A 639 "
            pdb=" OG1 THR A 643 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OG1 THR A 436 "
            pdb=" OG1 THR A 441 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OD1 ASN A 460 "
            pdb=" OG1 THR A 484 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   PRO Y 268 "
            pdb=" NE2 GLN Y 330 "
     model   vdw
     2.322 3.120
  ... (remaining 79728 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=0.50 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:             2.240
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.290
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
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      :  0.006   0.063  10297  Z= 0.260
  Angle     :  1.082  19.391  13907  Z= 0.596
  Chirality :  0.061   0.338   1587
  Planarity :  0.007   0.082   1778
  Dihedral  : 11.156 117.367   3846
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.13 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.16 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    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: -3.95 (0.18), residues: 1261
  helix: -2.28 (0.14), residues: 809
  sheet: -2.31 (0.53), residues: 73
  loop : -3.03 (0.25), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 735 
 TYR   0.040   0.003   TYR A 174 
 PHE   0.040   0.003   PHE A  48 
 TRP   0.020   0.002   TRP Y  98 
 HIS   0.016   0.002   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (10297)
  covalent geometry    : angle       1.08235 (13907)
  hydrogen bonds       : bond        0.10585 (  613)
  hydrogen bonds       : angle       5.99034 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 276
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A   33 TYR cc_start: 0.6443 (m-10) cc_final: 0.5895 (m-80)
REVERT: A  400 ARG cc_start: 0.6653 (ptt90) cc_final: 0.5597 (ptm-80)
REVERT: A  531 ASP cc_start: 0.7900 (m-30) cc_final: 0.7694 (p0)
REVERT: A  563 MET cc_start: 0.3124 (ppp) cc_final: 0.2514 (mmp)
REVERT: A  573 MET cc_start: 0.6587 (ptp) cc_final: 0.5850 (ppp)
REVERT: A  671 LEU cc_start: 0.8352 (tp) cc_final: 0.8150 (tp)
REVERT: A  690 ASP cc_start: 0.8064 (m-30) cc_final: 0.7682 (m-30)
REVERT: Y  116 PHE cc_start: 0.8456 (t80) cc_final: 0.8193 (t80)
REVERT: Y  365 TYR cc_start: 0.5433 (m-10) cc_final: 0.5223 (m-10)
REVERT: E    3 ARG cc_start: 0.7175 (ttm170) cc_final: 0.6843 (ttt90)
REVERT: E   24 LYS cc_start: 0.8555 (ptpp) cc_final: 0.8285 (ptmm)
REVERT: B    4 LYS cc_start: 0.3563 (pttp) cc_final: 0.2883 (mttm)
  outliers start: 2
  outliers final: 1
  residues processed: 278
  average time/residue: 0.1231
  time to fit residues: 46.3825
Evaluate side-chains
  167 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue  203 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    0.0370
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:   10.0000
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  17 ASN
A 155 ASN
A 238 ASN
A 347 ASN
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 456 HIS
A 536 GLN
A 570 GLN
A 622 ASN
Y 196 ASN
Y 236 GLN
** Y 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 308 HIS
Y 355 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.195574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.141398 restraints weight = 12544.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.64
r_work: 0.3604 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10297  Z= 0.165
  Angle     :  0.708  12.431  13907  Z= 0.366
  Chirality :  0.045   0.233   1587
  Planarity :  0.005   0.070   1778
  Dihedral  :  6.502 106.454   1401
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.10 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.22), residues: 1261
  helix: -0.44 (0.17), residues: 821
  sheet: -2.15 (0.52), residues: 79
  loop : -2.54 (0.27), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 523 
 TYR   0.015   0.002   TYR A 364 
 PHE   0.023   0.002   PHE A 774 
 TRP   0.009   0.001   TRP Y  98 
 HIS   0.006   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (10297)
  covalent geometry    : angle       0.70775 (13907)
  hydrogen bonds       : bond        0.04709 (  613)
  hydrogen bonds       : angle       4.69076 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 179
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 TYR cc_start: 0.7866 (t80) cc_final: 0.7564 (t80)
REVERT: A  531 ASP cc_start: 0.8336 (m-30) cc_final: 0.7756 (p0)
REVERT: A  563 MET cc_start: 0.3667 (ppp) cc_final: 0.2894 (mmp)
REVERT: A  573 MET cc_start: 0.6962 (ptp) cc_final: 0.6546 (ppp)
REVERT: A  584 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.6954 (ptt180)
REVERT: A  690 ASP cc_start: 0.8260 (m-30) cc_final: 0.7893 (m-30)
REVERT: A  698 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8126 (pp20)
REVERT: Y  183 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7673 (mp)
REVERT: E    3 ARG cc_start: 0.7365 (ttm170) cc_final: 0.7042 (tmt170)
REVERT: E    9 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8311 (mmtt)
REVERT: E   24 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8345 (mmmt)
REVERT: B    4 LYS cc_start: 0.3396 (pttp) cc_final: 0.2791 (mttt)
  outliers start: 21
  outliers final: 9
  residues processed: 193
  average time/residue: 0.0999
  time to fit residues: 27.9843
Evaluate side-chains
  166 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 156
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  160 SER
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain Y residue  183 ILE
Chi-restraints excluded: chain Y residue  308 HIS
Chi-restraints excluded: chain Y residue  319 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 123 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 78 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 99 optimal weight:    0.4980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y   7 ASN
Y  47 GLN
** Y 244 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 = 0.4378 r_free = 0.4378 target = 0.194217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.140963 restraints weight = 12586.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 2.50
r_work: 0.3590 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3602
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3602
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10297  Z= 0.162
  Angle     :  0.680   9.897  13907  Z= 0.349
  Chirality :  0.044   0.209   1587
  Planarity :  0.004   0.067   1778
  Dihedral  :  6.107  97.635   1399
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.95 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.23), residues: 1261
  helix:  0.21 (0.18), residues: 818
  sheet: -1.87 (0.55), residues: 87
  loop : -2.30 (0.29), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.016   0.002   TYR Y 245 
 PHE   0.021   0.002   PHE E  43 
 TRP   0.012   0.001   TRP Y  98 
 HIS   0.010   0.001   HIS Y 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (10297)
  covalent geometry    : angle       0.67996 (13907)
  hydrogen bonds       : bond        0.04468 (  613)
  hydrogen bonds       : angle       4.49785 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 170
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 PHE cc_start: 0.8420 (m-80) cc_final: 0.8135 (m-80)
REVERT: A  531 ASP cc_start: 0.8367 (m-30) cc_final: 0.7815 (p0)
REVERT: A  563 MET cc_start: 0.3808 (ppp) cc_final: 0.2940 (mmp)
REVERT: A  573 MET cc_start: 0.6812 (ptp) cc_final: 0.6210 (ppp)
REVERT: A  584 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7019 (ptt180)
REVERT: A  690 ASP cc_start: 0.8252 (m-30) cc_final: 0.7873 (m-30)
REVERT: A  706 GLU cc_start: 0.7336 (pm20) cc_final: 0.6661 (pm20)
REVERT: A  763 MET cc_start: 0.8136 (ttt) cc_final: 0.7916 (ttt)
REVERT: Y  165 TRP cc_start: 0.7629 (t60) cc_final: 0.7099 (t-100)
REVERT: Y  183 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7878 (mp)
REVERT: Y  197 GLN cc_start: 0.8317 (tt0) cc_final: 0.8069 (mm110)
REVERT: E    3 ARG cc_start: 0.7488 (ttm170) cc_final: 0.7070 (tmt170)
REVERT: E   24 LYS cc_start: 0.8903 (ptpp) cc_final: 0.8381 (mmmt)
REVERT: E   53 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7897 (mm-40)
REVERT: B    4 LYS cc_start: 0.3605 (pttp) cc_final: 0.2982 (mttm)
  outliers start: 16
  outliers final: 10
  residues processed: 180
  average time/residue: 0.0981
  time to fit residues: 25.6076
Evaluate side-chains
  164 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  207 ASP
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain Y residue  183 ILE
Chi-restraints excluded: chain Y residue  319 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 94 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 308 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.192897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.136865 restraints weight = 12601.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.59
r_work: 0.3555 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3564
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3564 r_free = 0.3564    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3564
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10297  Z= 0.170
  Angle     :  0.674   9.090  13907  Z= 0.346
  Chirality :  0.044   0.191   1587
  Planarity :  0.004   0.068   1778
  Dihedral  :  5.892  92.149   1399
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.80 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.23), residues: 1261
  helix:  0.49 (0.18), residues: 813
  sheet: -1.79 (0.55), residues: 87
  loop : -2.21 (0.29), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG Y 366 
 TYR   0.015   0.002   TYR A 364 
 PHE   0.024   0.002   PHE E  43 
 TRP   0.009   0.001   TRP Y  98 
 HIS   0.007   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (10297)
  covalent geometry    : angle       0.67414 (13907)
  hydrogen bonds       : bond        0.04391 (  613)
  hydrogen bonds       : angle       4.35450 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7445 (tt)
REVERT: A  248 LYS cc_start: 0.8568 (tmtt) cc_final: 0.8047 (tptp)
REVERT: A  513 HIS cc_start: 0.7447 (m-70) cc_final: 0.6853 (m90)
REVERT: A  531 ASP cc_start: 0.8370 (m-30) cc_final: 0.7843 (p0)
REVERT: A  563 MET cc_start: 0.3945 (ppp) cc_final: 0.2969 (mmp)
REVERT: A  573 MET cc_start: 0.7040 (ptp) cc_final: 0.6326 (ppp)
REVERT: A  584 ARG cc_start: 0.7757 (ttp-170) cc_final: 0.7139 (ptt180)
REVERT: A  586 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7046 (mm-30)
REVERT: A  690 ASP cc_start: 0.8281 (m-30) cc_final: 0.7895 (m-30)
REVERT: A  763 MET cc_start: 0.8228 (ttt) cc_final: 0.7959 (ttt)
REVERT: Y  165 TRP cc_start: 0.7648 (t60) cc_final: 0.7083 (t-100)
REVERT: Y  183 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7890 (mp)
REVERT: Y  197 GLN cc_start: 0.8359 (tt0) cc_final: 0.8102 (mm110)
REVERT: E    3 ARG cc_start: 0.7492 (ttm170) cc_final: 0.7103 (tmt170)
REVERT: E    9 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8354 (mmtt)
REVERT: E   24 LYS cc_start: 0.8924 (ptpp) cc_final: 0.8372 (mmmt)
REVERT: E   53 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7766 (mm-40)
REVERT: B    4 LYS cc_start: 0.3543 (pttp) cc_final: 0.2949 (mttm)
  outliers start: 20
  outliers final: 14
  residues processed: 178
  average time/residue: 0.0961
  time to fit residues: 25.1076
Evaluate side-chains
  169 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain Y residue  183 ILE
Chi-restraints excluded: chain Y residue  308 HIS
Chi-restraints excluded: chain Y residue  319 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   chunk 98 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 108 optimal weight:    0.4980
   chunk 64 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0270
   chunk 76 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 133 ASN
** Y 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 308 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.194869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.143585 restraints weight = 12538.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 2.31
r_work: 0.3586 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3602
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3602
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10297  Z= 0.141
  Angle     :  0.658  10.068  13907  Z= 0.332
  Chirality :  0.043   0.200   1587
  Planarity :  0.004   0.065   1778
  Dihedral  :  5.614  83.320   1399
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.36 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.24), residues: 1261
  helix:  0.69 (0.18), residues: 820
  sheet: -1.69 (0.57), residues: 85
  loop : -2.03 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG Y 366 
 TYR   0.013   0.001   TYR Y 130 
 PHE   0.026   0.001   PHE E  43 
 TRP   0.012   0.001   TRP Y  98 
 HIS   0.005   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10297)
  covalent geometry    : angle       0.65775 (13907)
  hydrogen bonds       : bond        0.04064 (  613)
  hydrogen bonds       : angle       4.25519 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7402 (tt)
REVERT: A  531 ASP cc_start: 0.8373 (m-30) cc_final: 0.7800 (p0)
REVERT: A  563 MET cc_start: 0.4238 (ppp) cc_final: 0.3135 (mmp)
REVERT: A  573 MET cc_start: 0.7038 (ptp) cc_final: 0.6343 (ppp)
REVERT: A  584 ARG cc_start: 0.7744 (ttp-170) cc_final: 0.7498 (ttp-170)
REVERT: A  586 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6737 (mt-10)
REVERT: A  642 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7726 (t80)
REVERT: A  690 ASP cc_start: 0.8310 (m-30) cc_final: 0.7952 (m-30)
REVERT: Y   24 MET cc_start: 0.7695 (mmm) cc_final: 0.7403 (ttt)
REVERT: Y  183 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (mp)
REVERT: Y  197 GLN cc_start: 0.8313 (tt0) cc_final: 0.8103 (mm110)
REVERT: Y  258 HIS cc_start: 0.7812 (m-70) cc_final: 0.7333 (m90)
REVERT: E    3 ARG cc_start: 0.7487 (ttm170) cc_final: 0.7103 (tmt170)
REVERT: E   24 LYS cc_start: 0.8871 (ptpp) cc_final: 0.8363 (mmmt)
REVERT: B    4 LYS cc_start: 0.3584 (pttp) cc_final: 0.2912 (mttt)
  outliers start: 22
  outliers final: 14
  residues processed: 183
  average time/residue: 0.0849
  time to fit residues: 23.3782
Evaluate side-chains
  175 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain Y residue  183 ILE
Chi-restraints excluded: chain Y residue  308 HIS
Chi-restraints excluded: chain Y residue  319 ILE
Chi-restraints excluded: chain Y residue  378 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 113 optimal weight:    0.0870
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 22 optimal weight:    0.7980
   chunk 118 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 736 GLN
** Y 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 308 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.195995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.143518 restraints weight = 12712.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.64
r_work: 0.3580 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10297  Z= 0.137
  Angle     :  0.653   9.807  13907  Z= 0.329
  Chirality :  0.043   0.196   1587
  Planarity :  0.004   0.066   1778
  Dihedral  :  5.419  76.567   1399
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.63 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.24), residues: 1261
  helix:  0.89 (0.19), residues: 815
  sheet: -1.60 (0.57), residues: 85
  loop : -1.94 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG Y 366 
 TYR   0.014   0.001   TYR Y 130 
 PHE   0.029   0.002   PHE E  43 
 TRP   0.004   0.001   TRP Y 165 
 HIS   0.005   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10297)
  covalent geometry    : angle       0.65273 (13907)
  hydrogen bonds       : bond        0.03935 (  613)
  hydrogen bonds       : angle       4.20405 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7883 (m-30) cc_final: 0.7655 (t0)
REVERT: A  108 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7328 (tt)
REVERT: A  248 LYS cc_start: 0.8579 (tmtt) cc_final: 0.8166 (tptp)
REVERT: A  531 ASP cc_start: 0.8479 (m-30) cc_final: 0.7852 (p0)
REVERT: A  557 MET cc_start: 0.8301 (mmm) cc_final: 0.7598 (ppp)
REVERT: A  563 MET cc_start: 0.4227 (ppp) cc_final: 0.3033 (mmp)
REVERT: A  573 MET cc_start: 0.7062 (ptp) cc_final: 0.6299 (ppp)
REVERT: A  584 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7413 (ttp-170)
REVERT: A  586 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6670 (mt-10)
REVERT: A  642 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7793 (t80)
REVERT: A  690 ASP cc_start: 0.8298 (m-30) cc_final: 0.7941 (m-30)
REVERT: Y    9 MET cc_start: 0.5234 (ttt) cc_final: 0.4947 (ttm)
REVERT: Y  183 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7821 (mp)
REVERT: Y  197 GLN cc_start: 0.8319 (tt0) cc_final: 0.8085 (mm110)
REVERT: Y  258 HIS cc_start: 0.7836 (m-70) cc_final: 0.7351 (m90)
REVERT: Y  308 HIS cc_start: 0.5327 (OUTLIER) cc_final: 0.4121 (m-70)
REVERT: E    3 ARG cc_start: 0.7586 (ttm170) cc_final: 0.7190 (tmt170)
REVERT: E    9 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8301 (mmtt)
REVERT: E   24 LYS cc_start: 0.8866 (ptpp) cc_final: 0.8359 (mmmt)
REVERT: E   49 LEU cc_start: 0.9090 (mp) cc_final: 0.8867 (mp)
REVERT: E   53 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7844 (mm-40)
REVERT: B    4 LYS cc_start: 0.3525 (pttp) cc_final: 0.2815 (mttt)
REVERT: B   53 TYR cc_start: 0.7714 (t80) cc_final: 0.7491 (t80)
  outliers start: 24
  outliers final: 13
  residues processed: 177
  average time/residue: 0.0896
  time to fit residues: 23.8208
Evaluate side-chains
  173 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain Y residue  183 ILE
Chi-restraints excluded: chain Y residue  308 HIS
Chi-restraints excluded: chain Y residue  319 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 59 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0570
   chunk 64 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   chunk 118 optimal weight:    0.0270
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.3356

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y   7 ASN
** Y 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 308 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.196437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.143719 restraints weight = 12599.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.57
r_work: 0.3620 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10297  Z= 0.130
  Angle     :  0.652  10.762  13907  Z= 0.327
  Chirality :  0.042   0.196   1587
  Planarity :  0.004   0.066   1778
  Dihedral  :  5.327  72.273   1399
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.28 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.24), residues: 1261
  helix:  0.97 (0.19), residues: 817
  sheet: -1.57 (0.57), residues: 85
  loop : -1.81 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG Y 366 
 TYR   0.014   0.001   TYR Y 130 
 PHE   0.031   0.001   PHE E  43 
 TRP   0.017   0.001   TRP Y  98 
 HIS   0.012   0.001   HIS Y 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10297)
  covalent geometry    : angle       0.65198 (13907)
  hydrogen bonds       : bond        0.03806 (  613)
  hydrogen bonds       : angle       4.18313 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7872 (m-30) cc_final: 0.7655 (t0)
REVERT: A  108 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7216 (tt)
REVERT: A  248 LYS cc_start: 0.8511 (tmtt) cc_final: 0.8101 (tptp)
REVERT: A  531 ASP cc_start: 0.8454 (m-30) cc_final: 0.7856 (p0)
REVERT: A  557 MET cc_start: 0.8391 (mmm) cc_final: 0.7955 (ppp)
REVERT: A  563 MET cc_start: 0.4127 (ppp) cc_final: 0.2935 (mmp)
REVERT: A  573 MET cc_start: 0.7062 (ptp) cc_final: 0.6299 (ppp)
REVERT: A  586 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6735 (mt-10)
REVERT: A  690 ASP cc_start: 0.8274 (m-30) cc_final: 0.7929 (m-30)
REVERT: Y    9 MET cc_start: 0.5288 (ttt) cc_final: 0.4947 (ttm)
REVERT: Y   24 MET cc_start: 0.7714 (mmm) cc_final: 0.7421 (ttt)
REVERT: Y  183 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7832 (mp)
REVERT: Y  197 GLN cc_start: 0.8329 (tt0) cc_final: 0.8107 (mm110)
REVERT: Y  258 HIS cc_start: 0.7745 (m-70) cc_final: 0.7238 (m90)
REVERT: Y  308 HIS cc_start: 0.5510 (OUTLIER) cc_final: 0.4797 (m-70)
REVERT: E    3 ARG cc_start: 0.7412 (ttm170) cc_final: 0.7033 (tmt170)
REVERT: E    9 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8317 (mmtt)
REVERT: E   24 LYS cc_start: 0.8835 (ptpp) cc_final: 0.8295 (mmmt)
REVERT: B    4 LYS cc_start: 0.3774 (pttp) cc_final: 0.3080 (mttm)
REVERT: B   53 TYR cc_start: 0.7600 (t80) cc_final: 0.7363 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 177
  average time/residue: 0.0910
  time to fit residues: 23.9497
Evaluate side-chains
  170 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 156
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain Y residue  183 ILE
Chi-restraints excluded: chain Y residue  308 HIS
Chi-restraints excluded: chain Y residue  319 ILE
Chi-restraints excluded: chain Y residue  378 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 97 optimal weight:    0.0570
   chunk 51 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 114 optimal weight:    0.4980
   chunk 24 optimal weight:    0.2980
   chunk 20 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 122 optimal weight:    5.9990
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 101 GLN
Y 308 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.196065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.143340 restraints weight = 12522.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.52
r_work: 0.3599 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3599 r_free = 0.3599    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10297  Z= 0.136
  Angle     :  0.659  12.014  13907  Z= 0.330
  Chirality :  0.043   0.196   1587
  Planarity :  0.004   0.067   1778
  Dihedral  :  5.258  68.921   1399
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.93 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.24), residues: 1261
  helix:  0.98 (0.19), residues: 821
  sheet: -1.48 (0.58), residues: 85
  loop : -1.77 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Y 366 
 TYR   0.014   0.001   TYR Y 130 
 PHE   0.036   0.002   PHE Y 132 
 TRP   0.014   0.001   TRP Y  98 
 HIS   0.006   0.001   HIS Y 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10297)
  covalent geometry    : angle       0.65877 (13907)
  hydrogen bonds       : bond        0.03819 (  613)
  hydrogen bonds       : angle       4.17394 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7894 (m-30) cc_final: 0.7673 (t0)
REVERT: A  108 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7277 (tt)
REVERT: A  248 LYS cc_start: 0.8507 (tmtt) cc_final: 0.8113 (tptp)
REVERT: A  513 HIS cc_start: 0.7370 (m-70) cc_final: 0.7046 (m-70)
REVERT: A  531 ASP cc_start: 0.8464 (m-30) cc_final: 0.7860 (p0)
REVERT: A  557 MET cc_start: 0.8409 (mmm) cc_final: 0.7953 (ppp)
REVERT: A  563 MET cc_start: 0.4174 (ppp) cc_final: 0.2923 (mmp)
REVERT: A  573 MET cc_start: 0.7083 (ptp) cc_final: 0.6280 (ppp)
REVERT: A  586 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6673 (mt-10)
REVERT: A  688 ILE cc_start: 0.8944 (mm) cc_final: 0.8660 (mt)
REVERT: A  690 ASP cc_start: 0.8274 (m-30) cc_final: 0.7917 (m-30)
REVERT: Y    9 MET cc_start: 0.5299 (ttt) cc_final: 0.5081 (ttm)
REVERT: Y   72 MET cc_start: 0.5658 (tpp) cc_final: 0.5321 (tpp)
REVERT: Y  183 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7895 (mp)
REVERT: Y  197 GLN cc_start: 0.8344 (tt0) cc_final: 0.8096 (mm110)
REVERT: Y  258 HIS cc_start: 0.7714 (m-70) cc_final: 0.7208 (m90)
REVERT: E    3 ARG cc_start: 0.7459 (ttm170) cc_final: 0.7079 (tmt170)
REVERT: E    9 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8404 (mmtt)
REVERT: E   24 LYS cc_start: 0.8834 (ptpp) cc_final: 0.8301 (mmmt)
REVERT: B    4 LYS cc_start: 0.3618 (pttp) cc_final: 0.2938 (mttm)
REVERT: B   53 TYR cc_start: 0.7654 (t80) cc_final: 0.7435 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 170
  average time/residue: 0.0899
  time to fit residues: 22.6358
Evaluate side-chains
  169 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  183 ILE
Chi-restraints excluded: chain Y residue  308 HIS
Chi-restraints excluded: chain Y residue  319 ILE
Chi-restraints excluded: chain Y residue  378 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 115 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 116 optimal weight:    0.0980
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 107 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 308 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.195014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.142021 restraints weight = 12651.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 2.65
r_work: 0.3582 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10297  Z= 0.146
  Angle     :  0.668  11.572  13907  Z= 0.335
  Chirality :  0.043   0.195   1587
  Planarity :  0.004   0.067   1778
  Dihedral  :  5.227  66.460   1399
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.11 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.24), residues: 1261
  helix:  0.98 (0.18), residues: 821
  sheet: -1.45 (0.58), residues: 85
  loop : -1.72 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 525 
 TYR   0.014   0.001   TYR Y 130 
 PHE   0.034   0.001   PHE E  43 
 TRP   0.009   0.001   TRP Y  98 
 HIS   0.009   0.001   HIS Y 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10297)
  covalent geometry    : angle       0.66822 (13907)
  hydrogen bonds       : bond        0.03896 (  613)
  hydrogen bonds       : angle       4.19242 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7367 (tt)
REVERT: A  248 LYS cc_start: 0.8491 (tmtt) cc_final: 0.8098 (tptp)
REVERT: A  513 HIS cc_start: 0.7349 (m-70) cc_final: 0.7022 (m-70)
REVERT: A  531 ASP cc_start: 0.8463 (m-30) cc_final: 0.7858 (p0)
REVERT: A  557 MET cc_start: 0.8382 (mmm) cc_final: 0.7810 (ppp)
REVERT: A  563 MET cc_start: 0.4192 (ppp) cc_final: 0.2902 (mmp)
REVERT: A  573 MET cc_start: 0.7034 (ptp) cc_final: 0.6185 (ppp)
REVERT: A  586 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6590 (mt-10)
REVERT: A  690 ASP cc_start: 0.8254 (m-30) cc_final: 0.7892 (m-30)
REVERT: Y    9 MET cc_start: 0.5258 (ttt) cc_final: 0.5044 (ttm)
REVERT: Y   24 MET cc_start: 0.7712 (mmm) cc_final: 0.7443 (ttt)
REVERT: Y   72 MET cc_start: 0.5675 (tpp) cc_final: 0.5318 (tpp)
REVERT: Y  183 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7949 (mp)
REVERT: Y  197 GLN cc_start: 0.8336 (tt0) cc_final: 0.8106 (mm110)
REVERT: Y  258 HIS cc_start: 0.7721 (m-70) cc_final: 0.7194 (m90)
REVERT: E    3 ARG cc_start: 0.7572 (ttm170) cc_final: 0.7161 (ttp80)
REVERT: E    9 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8344 (mmtt)
REVERT: E   24 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8306 (mmmt)
REVERT: B    4 LYS cc_start: 0.3642 (pttp) cc_final: 0.2949 (mttm)
  outliers start: 17
  outliers final: 11
  residues processed: 170
  average time/residue: 0.0942
  time to fit residues: 23.5853
Evaluate side-chains
  168 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain Y residue  183 ILE
Chi-restraints excluded: chain Y residue  319 ILE
Chi-restraints excluded: chain Y residue  378 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 33 optimal weight:    0.1980
   chunk 113 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 267 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.195545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.143796 restraints weight = 12453.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 2.46
r_work: 0.3609 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3618 r_free = 0.3618    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10297  Z= 0.143
  Angle     :  0.670  11.989  13907  Z= 0.334
  Chirality :  0.043   0.195   1587
  Planarity :  0.004   0.066   1778
  Dihedral  :  5.160  61.840   1399
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 17.58 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.24), residues: 1261
  helix:  1.01 (0.18), residues: 824
  sheet: -1.50 (0.58), residues: 85
  loop : -1.66 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 525 
 TYR   0.013   0.001   TYR Y 130 
 PHE   0.036   0.002   PHE E  43 
 TRP   0.007   0.001   TRP Y  98 
 HIS   0.006   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10297)
  covalent geometry    : angle       0.66997 (13907)
  hydrogen bonds       : bond        0.03889 (  613)
  hydrogen bonds       : angle       4.18601 ( 1809)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7353 (tt)
REVERT: A  248 LYS cc_start: 0.8502 (tmtt) cc_final: 0.8115 (tptp)
REVERT: A  351 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8360 (t)
REVERT: A  513 HIS cc_start: 0.7401 (m-70) cc_final: 0.7100 (m-70)
REVERT: A  531 ASP cc_start: 0.8384 (m-30) cc_final: 0.7847 (p0)
REVERT: A  557 MET cc_start: 0.8342 (mmm) cc_final: 0.7798 (ppp)
REVERT: A  563 MET cc_start: 0.4211 (ppp) cc_final: 0.2862 (mmp)
REVERT: A  573 MET cc_start: 0.7068 (ptp) cc_final: 0.6228 (ppp)
REVERT: A  586 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6557 (mt-10)
REVERT: A  688 ILE cc_start: 0.8956 (mm) cc_final: 0.8701 (mt)
REVERT: A  690 ASP cc_start: 0.8230 (m-30) cc_final: 0.7886 (m-30)
REVERT: Y    9 MET cc_start: 0.5265 (ttt) cc_final: 0.5056 (ttm)
REVERT: Y   24 MET cc_start: 0.7722 (mmm) cc_final: 0.7455 (ttt)
REVERT: Y   72 MET cc_start: 0.5983 (tpp) cc_final: 0.5672 (tpp)
REVERT: Y  183 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7968 (mp)
REVERT: Y  258 HIS cc_start: 0.7633 (m-70) cc_final: 0.7142 (m90)
REVERT: E    3 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7160 (ttp80)
REVERT: E    9 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8232 (mmtt)
REVERT: E   24 LYS cc_start: 0.8792 (ptpp) cc_final: 0.8327 (mmmt)
REVERT: B    4 LYS cc_start: 0.3659 (pttp) cc_final: 0.2922 (mttp)
  outliers start: 15
  outliers final: 10
  residues processed: 173
  average time/residue: 0.0935
  time to fit residues: 24.0053
Evaluate side-chains
  167 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain Y residue  181 ILE
Chi-restraints excluded: chain Y residue  183 ILE
Chi-restraints excluded: chain Y residue  378 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 124 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0870
   chunk 118 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 105 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 460 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 = 0.4381 r_free = 0.4381 target = 0.194799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.138295 restraints weight = 12548.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 2.22
r_work: 0.3606 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10297  Z= 0.154
  Angle     :  0.682  11.867  13907  Z= 0.341
  Chirality :  0.043   0.193   1587
  Planarity :  0.004   0.067   1778
  Dihedral  :  5.174  59.198   1399
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.04 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.24), residues: 1261
  helix:  0.98 (0.18), residues: 824
  sheet: -1.50 (0.58), residues: 85
  loop : -1.63 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Y 366 
 TYR   0.014   0.001   TYR Y 130 
 PHE   0.034   0.001   PHE E  43 
 TRP   0.006   0.001   TRP Y  98 
 HIS   0.006   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10297)
  covalent geometry    : angle       0.68174 (13907)
  hydrogen bonds       : bond        0.03994 (  613)
  hydrogen bonds       : angle       4.20466 ( 1809)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3337.89 seconds
wall clock time: 57 minutes 46.81 seconds (3466.81 seconds total)