Starting phenix.real_space_refine
on Mon Jul 28 10:00:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xhb_33193/07_2025/7xhb_33193.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xhb_33193/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xhb_33193/07_2025/7xhb_33193.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xhb_33193/07_2025/7xhb_33193.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xhb_33193/07_2025/7xhb_33193.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xhb_33193/07_2025/7xhb_33193.cif"
  }
  resolution = 3.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.81, per 1000 atoms: 0.77
  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: 2.39
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.09
  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: 3.10

  Time building geometry restraints manager: 2.86 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:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.800
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.940
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.020   0.002   TRP Y  98 
 HIS   0.016   0.002   HIS A 297 
 PHE   0.040   0.003   PHE A  48 
 TYR   0.040   0.003   TYR A 174 
 ARG   0.005   0.001   ARG A 735 

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

*********************** 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  : 1.130 
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: 0.2643
  time to fit residues: 99.4991
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  : 1.132 
-------------------------------------------------------------------------------
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 105 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 50 optimal weight:    0.7980
   chunk 97 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  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 = 0.4391 r_free = 0.4391 target = 0.195679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.146158 restraints weight = 12381.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 2.39
r_work: 0.3617 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    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 = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.2292

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= 0.164
  Angle     :  0.708  12.535  13907  Z= 0.366
  Chirality :  0.044   0.233   1587
  Planarity :  0.005   0.070   1778
  Dihedral  :  6.452 104.980   1401
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 11.01 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.22), residues: 1261
  helix: -0.43 (0.17), residues: 821
  sheet: -2.08 (0.52), residues: 87
  loop : -2.54 (0.27), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP Y  98 
 HIS   0.006   0.001   HIS A 297 
 PHE   0.021   0.002   PHE E  39 
 TYR   0.015   0.002   TYR Y 130 
 ARG   0.008   0.001   ARG A 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04705 (  613)
  hydrogen bonds       : angle       4.66328 ( 1809)
  covalent geometry    : bond        0.00363 (10297)
  covalent geometry    : angle       0.70813 (13907)

*********************** 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
  201 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 TYR cc_start: 0.7848 (t80) cc_final: 0.7536 (t80)
REVERT: A  531 ASP cc_start: 0.8329 (m-30) cc_final: 0.7764 (p0)
REVERT: A  563 MET cc_start: 0.3475 (ppp) cc_final: 0.2856 (mmp)
REVERT: A  573 MET cc_start: 0.6934 (ptp) cc_final: 0.6549 (ppp)
REVERT: A  584 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.6973 (ptt180)
REVERT: A  690 ASP cc_start: 0.8249 (m-30) cc_final: 0.7899 (m-30)
REVERT: A  698 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8107 (pp20)
REVERT: Y  183 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7771 (mp)
REVERT: Y  197 GLN cc_start: 0.8276 (tt0) cc_final: 0.7955 (mm110)
REVERT: E    3 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7054 (tmt170)
REVERT: E    9 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8331 (mmtt)
REVERT: E   24 LYS cc_start: 0.8902 (ptpp) cc_final: 0.8356 (mmmt)
REVERT: B    4 LYS cc_start: 0.3424 (pttp) cc_final: 0.2806 (mttt)
  outliers start: 23
  outliers final: 10
  residues processed: 192
  average time/residue: 0.2167
  time to fit residues: 59.5329
Evaluate side-chains
  165 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
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  232 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 70 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 118 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 4 optimal weight:    0.3980
   chunk 68 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4387 r_free = 0.4387 target = 0.195230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.139628 restraints weight = 12572.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.19
r_work: 0.3625 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3489
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3489 r_free = 0.3489    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3489 r_free = 0.3489    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3489
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10297  Z= 0.150
  Angle     :  0.672   9.889  13907  Z= 0.344
  Chirality :  0.043   0.206   1587
  Planarity :  0.004   0.067   1778
  Dihedral  :  6.043  96.061   1399
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.67 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.23), residues: 1261
  helix:  0.23 (0.18), residues: 817
  sheet: -1.80 (0.55), residues: 86
  loop : -2.33 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP Y  98 
 HIS   0.010   0.001   HIS Y 308 
 PHE   0.023   0.002   PHE E   8 
 TYR   0.015   0.001   TYR Y 130 
 ARG   0.003   0.000   ARG A 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04340 (  613)
  hydrogen bonds       : angle       4.45214 ( 1809)
  covalent geometry    : bond        0.00328 (10297)
  covalent geometry    : angle       0.67191 (13907)

*********************** 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
  189 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 PHE cc_start: 0.8461 (m-80) cc_final: 0.8216 (m-80)
REVERT: A  248 LYS cc_start: 0.8636 (tmtt) cc_final: 0.8179 (tptp)
REVERT: A  531 ASP cc_start: 0.8470 (m-30) cc_final: 0.7899 (p0)
REVERT: A  563 MET cc_start: 0.3846 (ppp) cc_final: 0.2965 (mmp)
REVERT: A  573 MET cc_start: 0.7057 (ptp) cc_final: 0.6345 (ppp)
REVERT: A  584 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7023 (ptt180)
REVERT: A  665 TYR cc_start: 0.8149 (m-80) cc_final: 0.7937 (m-10)
REVERT: A  690 ASP cc_start: 0.8332 (m-30) cc_final: 0.7979 (m-30)
REVERT: A  698 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8302 (pp20)
REVERT: A  706 GLU cc_start: 0.7461 (pm20) cc_final: 0.6789 (pm20)
REVERT: Y  165 TRP cc_start: 0.7690 (t60) cc_final: 0.7150 (t-100)
REVERT: Y  183 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8046 (mp)
REVERT: Y  197 GLN cc_start: 0.8362 (tt0) cc_final: 0.8088 (mm110)
REVERT: E    3 ARG cc_start: 0.7515 (ttm170) cc_final: 0.7093 (tmt170)
REVERT: E    9 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8528 (mmtt)
REVERT: E   24 LYS cc_start: 0.8948 (ptpp) cc_final: 0.8368 (mmmt)
REVERT: E   53 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7833 (mm-40)
REVERT: B    4 LYS cc_start: 0.3561 (pttp) cc_final: 0.2939 (mttm)
  outliers start: 18
  outliers final: 12
  residues processed: 181
  average time/residue: 0.2082
  time to fit residues: 54.5644
Evaluate side-chains
  170 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
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  689 MET
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 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 115 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0030
   chunk 17 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   overall best weight:    0.5988

-------------------------------------------------------------------------------
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 133 ASN
Y 236 GLN
** 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 = 0.4380 r_free = 0.4380 target = 0.194429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.141769 restraints weight = 12499.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 2.41
r_work: 0.3594 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    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 = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2984

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= 0.149
  Angle     :  0.656   8.276  13907  Z= 0.334
  Chirality :  0.044   0.191   1587
  Planarity :  0.004   0.066   1778
  Dihedral  :  5.773  89.331   1399
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.15 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.23), residues: 1261
  helix:  0.52 (0.18), residues: 822
  sheet: -1.74 (0.56), residues: 86
  loop : -2.14 (0.29), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP Y  98 
 HIS   0.006   0.001   HIS A 297 
 PHE   0.023   0.002   PHE E   8 
 TYR   0.014   0.002   TYR Y 130 
 ARG   0.012   0.000   ARG Y 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04167 (  613)
  hydrogen bonds       : angle       4.28370 ( 1809)
  covalent geometry    : bond        0.00332 (10297)
  covalent geometry    : angle       0.65595 (13907)

*********************** 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
  192 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 173
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7935 (m-30) cc_final: 0.7693 (t0)
REVERT: A  108 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7380 (tt)
REVERT: A  248 LYS cc_start: 0.8569 (tmtt) cc_final: 0.8083 (tptp)
REVERT: A  513 HIS cc_start: 0.7424 (m-70) cc_final: 0.6827 (m90)
REVERT: A  531 ASP cc_start: 0.8406 (m-30) cc_final: 0.7879 (p0)
REVERT: A  563 MET cc_start: 0.3994 (ppp) cc_final: 0.2981 (mmp)
REVERT: A  573 MET cc_start: 0.7045 (ptp) cc_final: 0.6365 (ppp)
REVERT: A  584 ARG cc_start: 0.7600 (ttp-170) cc_final: 0.7046 (ptt180)
REVERT: A  586 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6870 (mt-10)
REVERT: A  642 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7646 (t80)
REVERT: A  688 ILE cc_start: 0.8894 (mm) cc_final: 0.8683 (mt)
REVERT: A  690 ASP cc_start: 0.8317 (m-30) cc_final: 0.7938 (m-30)
REVERT: Y  165 TRP cc_start: 0.7639 (t60) cc_final: 0.7079 (t-100)
REVERT: Y  183 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7864 (mp)
REVERT: Y  197 GLN cc_start: 0.8329 (tt0) cc_final: 0.8109 (mm110)
REVERT: E    3 ARG cc_start: 0.7432 (ttm170) cc_final: 0.7074 (tmt170)
REVERT: E    9 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8302 (mmtt)
REVERT: E   24 LYS cc_start: 0.8826 (ptpp) cc_final: 0.8258 (mmmt)
REVERT: E   53 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7757 (mm-40)
REVERT: B    4 LYS cc_start: 0.3604 (pttp) cc_final: 0.2950 (mttt)
  outliers start: 19
  outliers final: 13
  residues processed: 183
  average time/residue: 0.2107
  time to fit residues: 55.9094
Evaluate side-chains
  172 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
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  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  689 MET
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 80 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 112 optimal weight:    0.6980
   chunk 119 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 84 optimal weight:    9.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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**
** 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 = 0.4372 r_free = 0.4372 target = 0.193532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.138894 restraints weight = 12492.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.55
r_work: 0.3561 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10297  Z= 0.165
  Angle     :  0.669  10.051  13907  Z= 0.339
  Chirality :  0.044   0.193   1587
  Planarity :  0.004   0.066   1778
  Dihedral  :  5.653  85.756   1399
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.52 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.24), residues: 1261
  helix:  0.66 (0.18), residues: 823
  sheet: -1.71 (0.57), residues: 86
  loop : -1.98 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Y 165 
 HIS   0.009   0.001   HIS Y 308 
 PHE   0.026   0.002   PHE E  43 
 TYR   0.014   0.002   TYR Y 245 
 ARG   0.011   0.000   ARG Y 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04263 (  613)
  hydrogen bonds       : angle       4.27710 ( 1809)
  covalent geometry    : bond        0.00375 (10297)
  covalent geometry    : angle       0.66850 (13907)

*********************** 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
  189 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7495 (tt)
REVERT: A  248 LYS cc_start: 0.8585 (tmtt) cc_final: 0.8095 (tptp)
REVERT: A  531 ASP cc_start: 0.8441 (m-30) cc_final: 0.7894 (p0)
REVERT: A  563 MET cc_start: 0.4226 (ppp) cc_final: 0.3126 (mmp)
REVERT: A  573 MET cc_start: 0.7070 (ptp) cc_final: 0.6373 (ppp)
REVERT: A  584 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7212 (ptt180)
REVERT: A  586 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6859 (mt-10)
REVERT: A  642 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7836 (t80)
REVERT: A  657 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8072 (tp)
REVERT: A  688 ILE cc_start: 0.8938 (mm) cc_final: 0.8694 (mt)
REVERT: A  690 ASP cc_start: 0.8284 (m-30) cc_final: 0.7928 (m-30)
REVERT: Y   24 MET cc_start: 0.7791 (mmm) cc_final: 0.7435 (ttt)
REVERT: Y  183 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7899 (mp)
REVERT: Y  197 GLN cc_start: 0.8315 (tt0) cc_final: 0.8098 (mm110)
REVERT: E    3 ARG cc_start: 0.7386 (ttm170) cc_final: 0.7086 (ttp80)
REVERT: E    9 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8215 (mmtt)
REVERT: E   24 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8368 (mmmt)
REVERT: E   53 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7893 (mm-40)
REVERT: B    4 LYS cc_start: 0.3590 (pttp) cc_final: 0.2912 (mttt)
  outliers start: 24
  outliers final: 14
  residues processed: 179
  average time/residue: 0.1933
  time to fit residues: 51.3678
Evaluate side-chains
  176 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
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  689 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 37 optimal weight:    0.4980
   chunk 88 optimal weight:    7.9990
   chunk 115 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 54 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 42 optimal weight:    7.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 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 = 0.4350 r_free = 0.4350 target = 0.191172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135249 restraints weight = 12675.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.68
r_work: 0.3504 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3523
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3523 r_free = 0.3523    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3523
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10297  Z= 0.203
  Angle     :  0.705  10.243  13907  Z= 0.359
  Chirality :  0.045   0.207   1587
  Planarity :  0.004   0.068   1778
  Dihedral  :  5.679  84.190   1399
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.08 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.24), residues: 1261
  helix:  0.71 (0.18), residues: 811
  sheet: -1.72 (0.57), residues: 87
  loop : -1.85 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Y 165 
 HIS   0.008   0.001   HIS A 297 
 PHE   0.026   0.002   PHE E  43 
 TYR   0.024   0.002   TYR Y 245 
 ARG   0.010   0.000   ARG Y 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04540 (  613)
  hydrogen bonds       : angle       4.34037 ( 1809)
  covalent geometry    : bond        0.00473 (10297)
  covalent geometry    : angle       0.70459 (13907)

*********************** 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
  193 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7639 (tt)
REVERT: A  531 ASP cc_start: 0.8417 (m-30) cc_final: 0.7873 (p0)
REVERT: A  563 MET cc_start: 0.4196 (ppp) cc_final: 0.3104 (mmp)
REVERT: A  573 MET cc_start: 0.7095 (ptp) cc_final: 0.5885 (ppp)
REVERT: A  584 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.7074 (ptt180)
REVERT: A  586 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7051 (mm-30)
REVERT: A  642 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.7993 (t80)
REVERT: A  657 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8040 (tp)
REVERT: A  688 ILE cc_start: 0.8953 (mm) cc_final: 0.8702 (mt)
REVERT: A  690 ASP cc_start: 0.8244 (m-30) cc_final: 0.7892 (m-30)
REVERT: Y    9 MET cc_start: 0.5323 (ttt) cc_final: 0.5012 (ttm)
REVERT: Y  183 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7923 (mp)
REVERT: Y  197 GLN cc_start: 0.8330 (tt0) cc_final: 0.8091 (mm110)
REVERT: Y  258 HIS cc_start: 0.7865 (m-70) cc_final: 0.7352 (m90)
REVERT: E    3 ARG cc_start: 0.7412 (ttm170) cc_final: 0.7124 (ttp80)
REVERT: E    9 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8268 (mmtt)
REVERT: E   24 LYS cc_start: 0.8900 (ptpp) cc_final: 0.8391 (mmmt)
REVERT: B    4 LYS cc_start: 0.3638 (pttp) cc_final: 0.2941 (mttt)
  outliers start: 26
  outliers final: 15
  residues processed: 183
  average time/residue: 0.2020
  time to fit residues: 53.9316
Evaluate side-chains
  180 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  109 THR
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  657 LEU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  689 MET
Chi-restraints excluded: chain A residue  736 GLN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 122 optimal weight:    5.9990
   chunk 89 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 6 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0970
   chunk 48 optimal weight:    0.9980
   chunk 13 optimal weight:    0.2980
   chunk 115 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.4383 r_free = 0.4383 target = 0.195058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.139747 restraints weight = 12799.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 2.64
r_work: 0.3580 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    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 = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3433

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= 0.139
  Angle     :  0.669   9.940  13907  Z= 0.336
  Chirality :  0.043   0.196   1587
  Planarity :  0.004   0.066   1778
  Dihedral  :  5.451  74.010   1399
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.00 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.24), residues: 1261
  helix:  0.85 (0.18), residues: 820
  sheet: -1.68 (0.57), residues: 86
  loop : -1.83 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP Y  98 
 HIS   0.005   0.001   HIS Y 308 
 PHE   0.031   0.001   PHE E  43 
 TYR   0.013   0.001   TYR Y 130 
 ARG   0.008   0.000   ARG Y 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04049 (  613)
  hydrogen bonds       : angle       4.23969 ( 1809)
  covalent geometry    : bond        0.00304 (10297)
  covalent geometry    : angle       0.66939 (13907)

*********************** 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
  183 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7508 (tt)
REVERT: A  248 LYS cc_start: 0.8614 (tmtt) cc_final: 0.8375 (tptp)
REVERT: A  531 ASP cc_start: 0.8430 (m-30) cc_final: 0.7848 (p0)
REVERT: A  563 MET cc_start: 0.4175 (ppp) cc_final: 0.3040 (mmp)
REVERT: A  573 MET cc_start: 0.6912 (ptp) cc_final: 0.5789 (ppp)
REVERT: A  584 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.7468 (ttp-170)
REVERT: A  586 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6711 (mt-10)
REVERT: A  642 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.8035 (t80)
REVERT: A  657 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8023 (tp)
REVERT: A  688 ILE cc_start: 0.8932 (mm) cc_final: 0.8678 (mt)
REVERT: A  690 ASP cc_start: 0.8257 (m-30) cc_final: 0.7898 (m-30)
REVERT: A  759 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8075 (ttm)
REVERT: Y    9 MET cc_start: 0.5186 (ttt) cc_final: 0.4916 (ttm)
REVERT: Y   24 MET cc_start: 0.7655 (mmm) cc_final: 0.7330 (ttt)
REVERT: Y  183 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7890 (mp)
REVERT: Y  197 GLN cc_start: 0.8333 (tt0) cc_final: 0.8091 (mm110)
REVERT: Y  258 HIS cc_start: 0.7838 (m-70) cc_final: 0.7375 (m90)
REVERT: E    3 ARG cc_start: 0.7461 (ttm170) cc_final: 0.7063 (ttt180)
REVERT: E    9 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8213 (mmtt)
REVERT: E   24 LYS cc_start: 0.8820 (ptpp) cc_final: 0.8325 (mmmt)
REVERT: E   53 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7866 (mm-40)
REVERT: B    4 LYS cc_start: 0.3649 (pttp) cc_final: 0.2907 (mttm)
  outliers start: 22
  outliers final: 16
  residues processed: 174
  average time/residue: 0.2070
  time to fit residues: 52.8750
Evaluate side-chains
  177 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 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  632 LYS
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  689 MET
Chi-restraints excluded: chain A residue  736 GLN
Chi-restraints excluded: chain A residue  759 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 119 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 107 optimal weight:    0.4980
   chunk 8 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0870
   chunk 104 optimal weight:    0.8980
   chunk 83 optimal weight:    6.9990
   chunk 105 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 308 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.194774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.143451 restraints weight = 12605.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 2.32
r_work: 0.3588 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3600
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3600 r_free = 0.3600    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 = 0.3600 r_free = 0.3600    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3600
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10297  Z= 0.144
  Angle     :  0.666  11.082  13907  Z= 0.333
  Chirality :  0.043   0.196   1587
  Planarity :  0.004   0.067   1778
  Dihedral  :  5.326  69.387   1399
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.65 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1261
  helix:  0.92 (0.18), residues: 819
  sheet: -1.50 (0.58), residues: 85
  loop : -1.72 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP Y  98 
 HIS   0.005   0.001   HIS A 297 
 PHE   0.033   0.002   PHE E  43 
 TYR   0.014   0.001   TYR Y 130 
 ARG   0.007   0.000   ARG Y 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  613)
  hydrogen bonds       : angle       4.18004 ( 1809)
  covalent geometry    : bond        0.00321 (10297)
  covalent geometry    : angle       0.66563 (13907)

*********************** 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
  179 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 1.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7468 (tt)
REVERT: A  248 LYS cc_start: 0.8562 (tmtt) cc_final: 0.8304 (tptp)
REVERT: A  531 ASP cc_start: 0.8395 (m-30) cc_final: 0.7849 (p0)
REVERT: A  563 MET cc_start: 0.4109 (ppp) cc_final: 0.2920 (mmp)
REVERT: A  573 MET cc_start: 0.6899 (ptp) cc_final: 0.5788 (ppp)
REVERT: A  586 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6705 (mt-10)
REVERT: A  657 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8011 (tp)
REVERT: A  688 ILE cc_start: 0.8945 (mm) cc_final: 0.8662 (mt)
REVERT: A  690 ASP cc_start: 0.8264 (m-30) cc_final: 0.7921 (m-30)
REVERT: Y    9 MET cc_start: 0.5306 (ttt) cc_final: 0.5099 (ttm)
REVERT: Y  132 PHE cc_start: 0.7738 (m-80) cc_final: 0.7000 (m-80)
REVERT: Y  139 MET cc_start: 0.2901 (ptt) cc_final: 0.2632 (ptt)
REVERT: Y  183 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7945 (mp)
REVERT: Y  197 GLN cc_start: 0.8313 (tt0) cc_final: 0.8091 (mm110)
REVERT: Y  258 HIS cc_start: 0.7734 (m-70) cc_final: 0.7281 (m90)
REVERT: Y  308 HIS cc_start: 0.5545 (OUTLIER) cc_final: 0.4614 (m-70)
REVERT: E    3 ARG cc_start: 0.7409 (ttm170) cc_final: 0.7049 (ttt180)
REVERT: E    9 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8147 (mmtt)
REVERT: E   24 LYS cc_start: 0.8768 (ptpp) cc_final: 0.8328 (mmmt)
REVERT: B    4 LYS cc_start: 0.3793 (pttp) cc_final: 0.3105 (mttm)
REVERT: B   53 TYR cc_start: 0.7665 (t80) cc_final: 0.7435 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 170
  average time/residue: 0.1951
  time to fit residues: 48.9285
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  : 1.059 
-------------------------------------------------------------------------------
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  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  632 LYS
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 A residue  689 MET
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  378 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 121 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 107 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4372 r_free = 0.4372 target = 0.193977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.141712 restraints weight = 12593.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 2.41
r_work: 0.3569 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    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 = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10297  Z= 0.156
  Angle     :  0.678  11.340  13907  Z= 0.339
  Chirality :  0.043   0.195   1587
  Planarity :  0.004   0.067   1778
  Dihedral  :  5.303  66.916   1399
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.74 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.24), residues: 1261
  helix:  0.92 (0.18), residues: 819
  sheet: -1.58 (0.58), residues: 86
  loop : -1.63 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Y 165 
 HIS   0.006   0.001   HIS A 297 
 PHE   0.033   0.002   PHE E  43 
 TYR   0.015   0.002   TYR Y 245 
 ARG   0.007   0.000   ARG Y 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04089 (  613)
  hydrogen bonds       : angle       4.20303 ( 1809)
  covalent geometry    : bond        0.00354 (10297)
  covalent geometry    : angle       0.67753 (13907)

*********************** 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
  177 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7522 (tt)
REVERT: A  248 LYS cc_start: 0.8555 (tmtt) cc_final: 0.8292 (tptp)
REVERT: A  531 ASP cc_start: 0.8413 (m-30) cc_final: 0.7854 (p0)
REVERT: A  563 MET cc_start: 0.4138 (ppp) cc_final: 0.2899 (mmp)
REVERT: A  573 MET cc_start: 0.6925 (ptp) cc_final: 0.5791 (ppp)
REVERT: A  586 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6699 (mt-10)
REVERT: A  688 ILE cc_start: 0.8932 (mm) cc_final: 0.8663 (mt)
REVERT: A  690 ASP cc_start: 0.8251 (m-30) cc_final: 0.7898 (m-30)
REVERT: Y    9 MET cc_start: 0.5235 (ttt) cc_final: 0.5014 (ttm)
REVERT: Y   24 MET cc_start: 0.7668 (mmm) cc_final: 0.7328 (ttt)
REVERT: Y  104 MET cc_start: 0.7912 (mmm) cc_final: 0.7593 (mmm)
REVERT: Y  132 PHE cc_start: 0.7807 (m-80) cc_final: 0.7038 (m-80)
REVERT: Y  139 MET cc_start: 0.2966 (ptt) cc_final: 0.2764 (ptt)
REVERT: Y  183 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7950 (mp)
REVERT: Y  197 GLN cc_start: 0.8300 (tt0) cc_final: 0.8083 (mm110)
REVERT: Y  258 HIS cc_start: 0.7774 (m-70) cc_final: 0.7287 (m90)
REVERT: E    3 ARG cc_start: 0.7507 (ttm170) cc_final: 0.7080 (ttt180)
REVERT: E    9 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8164 (mmtt)
REVERT: E   24 LYS cc_start: 0.8785 (ptpp) cc_final: 0.8330 (mmmt)
REVERT: B    4 LYS cc_start: 0.3785 (pttp) cc_final: 0.3100 (mttm)
  outliers start: 18
  outliers final: 15
  residues processed: 170
  average time/residue: 0.1999
  time to fit residues: 50.2709
Evaluate side-chains
  172 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
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  266 MET
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  632 LYS
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  689 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 7 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 119 optimal weight:    0.6980
   chunk 55 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4367 r_free = 0.4367 target = 0.193382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.140068 restraints weight = 12570.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 2.50
r_work: 0.3559 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    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 = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.3663

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= 0.167
  Angle     :  0.693  11.751  13907  Z= 0.347
  Chirality :  0.044   0.194   1587
  Planarity :  0.004   0.067   1778
  Dihedral  :  5.311  64.951   1399
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.24), residues: 1261
  helix:  0.88 (0.18), residues: 825
  sheet: -1.60 (0.58), residues: 86
  loop : -1.65 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Y 165 
 HIS   0.008   0.001   HIS Y 308 
 PHE   0.036   0.002   PHE E  43 
 TYR   0.016   0.002   TYR Y 245 
 ARG   0.008   0.000   ARG Y 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04174 (  613)
  hydrogen bonds       : angle       4.24125 ( 1809)
  covalent geometry    : bond        0.00384 (10297)
  covalent geometry    : angle       0.69298 (13907)

********************** 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
  173 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7538 (tt)
REVERT: A  248 LYS cc_start: 0.8552 (tmtt) cc_final: 0.8286 (tptp)
REVERT: A  531 ASP cc_start: 0.8435 (m-30) cc_final: 0.7847 (p0)
REVERT: A  563 MET cc_start: 0.4193 (ppp) cc_final: 0.2909 (mmp)
REVERT: A  573 MET cc_start: 0.6982 (ptp) cc_final: 0.5841 (ppp)
REVERT: A  586 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6707 (mt-10)
REVERT: A  688 ILE cc_start: 0.8936 (mm) cc_final: 0.8662 (mt)
REVERT: A  690 ASP cc_start: 0.8261 (m-30) cc_final: 0.7908 (m-30)
REVERT: Y    9 MET cc_start: 0.5204 (ttt) cc_final: 0.4985 (ttm)
REVERT: Y   24 MET cc_start: 0.7669 (mmm) cc_final: 0.7319 (ttt)
REVERT: Y  104 MET cc_start: 0.7897 (mmm) cc_final: 0.7578 (mmm)
REVERT: Y  132 PHE cc_start: 0.7813 (m-80) cc_final: 0.7033 (m-80)
REVERT: Y  183 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7974 (mp)
REVERT: Y  197 GLN cc_start: 0.8312 (tt0) cc_final: 0.8093 (mm110)
REVERT: Y  258 HIS cc_start: 0.7743 (m-70) cc_final: 0.7205 (m90)
REVERT: Y  308 HIS cc_start: 0.5851 (OUTLIER) cc_final: 0.4932 (m-70)
REVERT: E    3 ARG cc_start: 0.7498 (ttm170) cc_final: 0.7054 (ttt180)
REVERT: E    9 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8223 (mmtt)
REVERT: E   24 LYS cc_start: 0.8817 (ptpp) cc_final: 0.8336 (mmmt)
REVERT: B    4 LYS cc_start: 0.3770 (pttp) cc_final: 0.3086 (mttm)
  outliers start: 17
  outliers final: 14
  residues processed: 166
  average time/residue: 0.1998
  time to fit residues: 49.3073
Evaluate side-chains
  171 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 154
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
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  266 MET
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  632 LYS
Chi-restraints excluded: chain A residue  651 GLU
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  685 LEU
Chi-restraints excluded: chain A residue  689 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 108 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 80 optimal weight:    0.2980
   chunk 52 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4374 r_free = 0.4374 target = 0.194221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.141550 restraints weight = 12523.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 2.50
r_work: 0.3576 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    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 = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10297  Z= 0.153
  Angle     :  0.690  11.952  13907  Z= 0.345
  Chirality :  0.044   0.194   1587
  Planarity :  0.004   0.066   1778
  Dihedral  :  5.279  62.359   1399
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.21 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1261
  helix:  0.90 (0.18), residues: 824
  sheet: -1.58 (0.58), residues: 86
  loop : -1.66 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP Y 165 
 HIS   0.006   0.001   HIS A 297 
 PHE   0.035   0.002   PHE E  43 
 TYR   0.014   0.002   TYR Y 130 
 ARG   0.007   0.000   ARG Y 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04080 (  613)
  hydrogen bonds       : angle       4.21344 ( 1809)
  covalent geometry    : bond        0.00347 (10297)
  covalent geometry    : angle       0.69048 (13907)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6700.80 seconds
wall clock time: 117 minutes 8.93 seconds (7028.93 seconds total)