Starting phenix.real_space_refine
on Tue Apr 29 23:25:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y93_39068/04_2025/8y93_39068.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y93_39068/04_2025/8y93_39068.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y93_39068/04_2025/8y93_39068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y93_39068/04_2025/8y93_39068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y93_39068/04_2025/8y93_39068.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y93_39068/04_2025/8y93_39068.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.055
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
     S      40      5.16       5
     Cl      1      4.86       5
     Na      1      4.78       5
     C    6072      2.51       5
     N    1413      2.21       5
     O    1528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9055
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "E"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 23
          Unusual residues: {' CL': 1, ' NA': 1, 'TP0': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.91, per 1000 atoms: 0.65
  Number of scatterers: 9055
  At special positions: 0
  Unit cell: (97.09, 85.41, 118.26, 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)
     Cl      1     17.00
     S      40     16.00
     Na      1     11.00
     O    1528      8.00
     N    1413      7.00
     C    6072      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: 2.34
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 0 sheets defined
      72.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 74
      removed outlier: 3.738A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 79
    Processing helix  chain 'A' and resid 81 through 89
    Processing helix  chain 'A' and resid 90 through 93
      removed outlier: 3.652A  pdb=" N   ALA A  93 " --> pdb=" O   GLY A  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 90 through 93'
    Processing helix  chain 'A' and resid 94 through 104
    Processing helix  chain 'A' and resid 106 through 120
      removed outlier: 4.085A  pdb=" N   GLU A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU A 114 " --> pdb=" O   PHE A 110 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 115 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLN A 118 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 165
      removed outlier: 3.644A  pdb=" N   GLY A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ASN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER A 165 " --> pdb=" O   TYR A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 234 through 253
      removed outlier: 3.863A  pdb=" N   CYS A 240 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 267
      removed outlier: 3.838A  pdb=" N   SER A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS A 261 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ILE A 265 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 282
      removed outlier: 3.611A  pdb=" N   PHE A 272 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.889A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 320
      removed outlier: 3.505A  pdb=" N   THR A 313 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 330
    Processing helix  chain 'A' and resid 338 through 372
      removed outlier: 3.699A  pdb=" N   ASP A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A 359 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA A 360 " --> pdb=" O   VAL A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 3.585A  pdb=" N   VAL A 387 " --> pdb=" O   GLY A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 397
      removed outlier: 3.863A  pdb=" N   THR A 397 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.632A  pdb=" N   TRP A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE A 409 " --> pdb=" O   ALA A 405 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASP A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER A 419 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 427 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASP A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 441
      removed outlier: 4.151A  pdb=" N   ARG A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   HIS A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 436 through 441'
    Processing helix  chain 'A' and resid 441 through 457
      removed outlier: 3.772A  pdb=" N   PHE A 447 " --> pdb=" O   LYS A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 494
      removed outlier: 4.435A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 510
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.918A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TRP A 556 " --> pdb=" O   PRO A 552 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET A 566 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 580
    Processing helix  chain 'A' and resid 583 through 589
    Processing helix  chain 'A' and resid 597 through 603
      removed outlier: 3.917A  pdb=" N   VAL A 601 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
      removed outlier: 3.792A  pdb=" N   PHE A 609 " --> pdb=" O   ILE A 606 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 606 through 609'
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 4.031A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 61 through 74
      removed outlier: 3.792A  pdb=" N   PHE E  65 " --> pdb=" O   LYS E  61 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU E  66 " --> pdb=" O   LYS E  62 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL E  70 " --> pdb=" O   LEU E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 105
    Processing helix  chain 'E' and resid 105 through 121
    Processing helix  chain 'E' and resid 131 through 134
    Processing helix  chain 'E' and resid 135 through 166
      removed outlier: 4.071A  pdb=" N   TYR E 139 " --> pdb=" O   LYS E 135 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR E 151 " --> pdb=" O   TYR E 147 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   VAL E 154 " --> pdb=" O   PHE E 150 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 215
    Processing helix  chain 'E' and resid 234 through 253
    Processing helix  chain 'E' and resid 255 through 267
    Processing helix  chain 'E' and resid 269 through 284
      removed outlier: 4.462A  pdb=" N   VAL E 273 " --> pdb=" O   LEU E 269 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LEU E 274 " --> pdb=" O   PRO E 270 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   THR E 283 " --> pdb=" O   VAL E 279 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU E 284 " --> pdb=" O   HIS E 280 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 295
      removed outlier: 4.048A  pdb=" N   ILE E 291 " --> pdb=" O   ALA E 287 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 308 through 320
      removed outlier: 3.639A  pdb=" N   ALA E 312 " --> pdb=" O   TRP E 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 324 through 333
      removed outlier: 3.745A  pdb=" N   TYR E 332 " --> pdb=" O   ALA E 328 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 338 through 372
    Processing helix  chain 'E' and resid 385 through 398
      Proline residue:  E 392  - end of helix
    Processing helix  chain 'E' and resid 400 through 435
    Processing helix  chain 'E' and resid 435 through 441
    Processing helix  chain 'E' and resid 441 through 457
    Processing helix  chain 'E' and resid 464 through 494
      removed outlier: 3.958A  pdb=" N   VAL E 468 " --> pdb=" O   GLY E 464 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 497 through 509
    Processing helix  chain 'E' and resid 514 through 523
    Processing helix  chain 'E' and resid 523 through 539
    Processing helix  chain 'E' and resid 551 through 567
      removed outlier: 4.024A  pdb=" N   ASN E 555 " --> pdb=" O   PRO E 551 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TRP E 556 " --> pdb=" O   PRO E 552 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER E 565 " --> pdb=" O   ILE E 561 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 567 through 580
    Processing helix  chain 'E' and resid 583 through 593
    Processing helix  chain 'E' and resid 598 through 603
      removed outlier: 3.933A  pdb=" N   ALA E 602 " --> pdb=" O   HIS E 598 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 610 through 616
      removed outlier: 4.066A  pdb=" N   TRP E 614 " --> pdb=" O   GLN E 610 " (cutoff:3.500A)

    527 hydrogen bonds defined for protein.
    1572 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: 2.51

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1395
        1.32 -     1.44: 2870
        1.44 -     1.57: 5022
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 9349
  Sorted by residual:
  bond pdb=" CA  TRP E 128 "
       pdb=" C   TRP E 128 "
    ideal  model  delta    sigma   weight residual
    1.530  1.458  0.072 1.14e-02 7.69e+03 4.02e+01
  bond pdb=" C3  TP0 A 701 "
       pdb=" C6  TP0 A 701 "
    ideal  model  delta    sigma   weight residual
    1.483  1.555 -0.072 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" CA  VAL E 127 "
       pdb=" C   VAL E 127 "
    ideal  model  delta    sigma   weight residual
    1.525  1.481  0.044 1.27e-02 6.20e+03 1.18e+01
  bond pdb=" CA  ILE E 130 "
       pdb=" C   ILE E 130 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 1.54e-02 4.22e+03 1.07e+01
  bond pdb=" CA  LYS E 129 "
       pdb=" C   LYS E 129 "
    ideal  model  delta    sigma   weight residual
    1.522  1.485  0.037 1.31e-02 5.83e+03 7.81e+00
  ... (remaining 9344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.42: 12716
        3.42 -     6.84: 36
        6.84 -    10.26: 1
       10.26 -    13.69: 3
       13.69 -    17.11: 1
  Bond angle restraints: 12757
  Sorted by residual:
  angle pdb=" N   LYS E 129 "
        pdb=" CA  LYS E 129 "
        pdb=" C   LYS E 129 "
      ideal   model   delta    sigma   weight residual
     113.30   96.19   17.11 1.34e+00 5.57e-01 1.63e+02
  angle pdb=" N   VAL E 127 "
        pdb=" CA  VAL E 127 "
        pdb=" C   VAL E 127 "
      ideal   model   delta    sigma   weight residual
     113.16  102.59   10.57 1.49e+00 4.50e-01 5.03e+01
  angle pdb=" N   ILE E 130 "
        pdb=" CA  ILE E 130 "
        pdb=" C   ILE E 130 "
      ideal   model   delta    sigma   weight residual
     112.83  106.53    6.30 9.90e-01 1.02e+00 4.04e+01
  angle pdb=" C14 TP0 A 701 "
        pdb=" N1  TP0 A 701 "
        pdb=" C20 TP0 A 701 "
      ideal   model   delta    sigma   weight residual
     111.01   99.00   12.01 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" N   VAL A 137 "
        pdb=" CA  VAL A 137 "
        pdb=" C   VAL A 137 "
      ideal   model   delta    sigma   weight residual
     113.00  108.42    4.58 1.30e+00 5.92e-01 1.24e+01
  ... (remaining 12752 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.77: 5099
       28.77 -    57.55: 111
       57.55 -    86.32: 8
       86.32 -   115.09: 1
      115.09 -   143.87: 2
  Dihedral angle restraints: 5221
    sinusoidal: 1957
      harmonic: 3264
  Sorted by residual:
  dihedral pdb=" C22 TP0 A 701 "
           pdb=" C21 TP0 A 701 "
           pdb=" C4  TP0 A 701 "
           pdb=" C6  TP0 A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      71.36  -72.51  143.87     1      3.00e+01 1.11e-03 1.93e+01
  dihedral pdb=" C10 TP0 A 701 "
           pdb=" C21 TP0 A 701 "
           pdb=" C4  TP0 A 701 "
           pdb=" C22 TP0 A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     108.73 -108.00 -143.27     1      3.00e+01 1.11e-03 1.92e+01
  dihedral pdb=" C   LYS E 129 "
           pdb=" N   LYS E 129 "
           pdb=" CA  LYS E 129 "
           pdb=" CB  LYS E 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.18   -9.42     0      2.50e+00 1.60e-01 1.42e+01
  ... (remaining 5218 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1156
       0.045 -    0.090: 231
       0.090 -    0.134: 28
       0.134 -    0.179: 1
       0.179 -    0.224: 2
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CB  VAL E 127 "
            pdb=" CA  VAL E 127 "
            pdb=" CG1 VAL E 127 "
            pdb=" CG2 VAL E 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  LYS E 129 "
            pdb=" N   LYS E 129 "
            pdb=" C   LYS E 129 "
            pdb=" CB  LYS E 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  TRP E 128 "
            pdb=" N   TRP E 128 "
            pdb=" C   TRP E 128 "
            pdb=" CB  TRP E 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.54e-01
  ... (remaining 1415 not shown)

  Planarity restraints: 1554
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS E 131 "   -0.031 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO E 132 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO E 132 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E 132 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 391 "    0.030 5.00e-02 4.00e+02   4.53e-02 3.29e+00
        pdb=" N   PRO E 392 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO E 392 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO E 392 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 127 "    0.008 2.00e-02 2.50e+03   1.53e-02 2.34e+00
        pdb=" C   VAL E 127 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   VAL E 127 "    0.010 2.00e-02 2.50e+03
        pdb=" N   TRP E 128 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1551 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 122
        2.68 -     3.24: 9022
        3.24 -     3.79: 14631
        3.79 -     4.35: 19640
        4.35 -     4.90: 32766
  Nonbonded interactions: 76181
  Sorted by model distance:
  nonbonded pdb=" C20 TP0 A 701 "
            pdb=" C29 TP0 A 701 "
     model   vdw
     2.127 3.088
  nonbonded pdb=" OG  SER A 318 "
            pdb="CL    CL A 703 "
     model   vdw
     2.227 3.190
  nonbonded pdb=" N   LYS E 129 "
            pdb=" N   ILE E 130 "
     model   vdw
     2.244 2.560
  nonbonded pdb=" O   SER A 251 "
            pdb=" OG1 THR A 258 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR E 332 "
            pdb=" OG1 THR E 429 "
     model   vdw
     2.295 3.040
  ... (remaining 76176 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 53 through 617)
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.190
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.740
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
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      :  0.003   0.072   9349  Z= 0.189
  Angle     :  0.603  17.108  12757  Z= 0.367
  Chirality :  0.035   0.224   1418
  Planarity :  0.004   0.048   1554
  Dihedral  : 11.793 143.867   3145
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  :  7.14 %
    Favored  : 87.71 %
  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: -1.85 (0.23), residues: 1126
  helix: -0.76 (0.18), residues: 730
  sheet:  None (None), residues: 0
  loop : -1.94 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 128 
 HIS   0.001   0.000   HIS A 280 
 PHE   0.011   0.001   PHE A 409 
 TYR   0.007   0.001   TYR A 340 
 ARG   0.002   0.000   ARG E 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14553 (  527)
  hydrogen bonds       : angle       6.59816 ( 1572)
  covalent geometry    : bond        0.00303 ( 9349)
  covalent geometry    : angle       0.60326 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 249
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A  147 TYR cc_start: 0.8334 (m-10) cc_final: 0.7725 (m-10)
REVERT: A  271 TYR cc_start: 0.8411 (m-80) cc_final: 0.8185 (m-80)
REVERT: A  348 SER cc_start: 0.8411 (m) cc_final: 0.8208 (m)
REVERT: A  439 LYS cc_start: 0.8491 (mttt) cc_final: 0.8103 (mtpm)
REVERT: A  585 TRP cc_start: 0.6791 (m100) cc_final: 0.6542 (m-10)
REVERT: A  611 LEU cc_start: 0.8222 (tp) cc_final: 0.7839 (tt)
REVERT: E  111 TYR cc_start: 0.8222 (t80) cc_final: 0.7846 (t80)
REVERT: E  120 ASN cc_start: 0.8206 (m-40) cc_final: 0.7990 (m-40)
REVERT: E  133 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.6754 (m-80)
REVERT: E  494 TRP cc_start: 0.7747 (m100) cc_final: 0.7422 (m100)
  outliers start: 49
  outliers final: 9
  residues processed: 279
  average time/residue: 0.8287
  time to fit residues: 254.3097
Evaluate side-chains
  160 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain E residue  131 CYS
Chi-restraints excluded: chain E residue  133 PHE
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  180 TRP
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  205 TYR
Chi-restraints excluded: chain E residue  359 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 33 optimal weight:    0.2980
   chunk 53 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 101 optimal weight:    0.2980
   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  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 153 ASN
A 184 ASN
A 280 HIS
A 350 ASN
A 507 GLN
E 120 ASN
E 153 ASN
E 337 ASN
E 613 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.183918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.153552 restraints weight = 12307.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 2.10
r_work: 0.3806 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3672 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9349  Z= 0.117
  Angle     :  0.570  10.544  12757  Z= 0.283
  Chirality :  0.039   0.160   1418
  Planarity :  0.004   0.032   1554
  Dihedral  :  8.020 140.482   1242
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 17.54 %
    Favored  : 77.94 %
  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: -0.28 (0.25), residues: 1126
  helix:  0.48 (0.19), residues: 753
  sheet:  None (None), residues: 0
  loop : -1.46 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 128 
 HIS   0.005   0.001   HIS E 372 
 PHE   0.021   0.001   PHE E 275 
 TYR   0.015   0.001   TYR A 111 
 ARG   0.006   0.001   ARG A 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  527)
  hydrogen bonds       : angle       4.42417 ( 1572)
  covalent geometry    : bond        0.00256 ( 9349)
  covalent geometry    : angle       0.56961 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 164
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
REVERT: A  250 PHE cc_start: 0.8382 (m-10) cc_final: 0.8050 (m-10)
REVERT: A  297 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7915 (pt)
REVERT: A  439 LYS cc_start: 0.8809 (mttt) cc_final: 0.8440 (mtpm)
REVERT: A  581 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7406 (tm-30)
REVERT: A  585 TRP cc_start: 0.7116 (m100) cc_final: 0.6583 (m-10)
REVERT: A  595 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7497 (mp0)
REVERT: E  100 LEU cc_start: 0.8323 (tt) cc_final: 0.7252 (mm)
REVERT: E  119 TYR cc_start: 0.6878 (t80) cc_final: 0.6447 (t80)
REVERT: E  120 ASN cc_start: 0.8303 (m110) cc_final: 0.8023 (m-40)
REVERT: E  242 MET cc_start: 0.7638 (mtm) cc_final: 0.7380 (mtt)
REVERT: E  436 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8226 (mp10)
REVERT: E  438 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8113 (mm)
REVERT: E  603 GLN cc_start: 0.6964 (mt0) cc_final: 0.6710 (mp10)
  outliers start: 43
  outliers final: 14
  residues processed: 189
  average time/residue: 0.8533
  time to fit residues: 178.4061
Evaluate side-chains
  147 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  581 GLN
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain E residue  180 TRP
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  436 GLN
Chi-restraints excluded: chain E residue  438 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 153 ASN
** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 350 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.177841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.146131 restraints weight = 12420.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 2.07
r_work: 0.3715 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9349  Z= 0.120
  Angle     :  0.563  15.884  12757  Z= 0.274
  Chirality :  0.038   0.136   1418
  Planarity :  0.004   0.029   1554
  Dihedral  :  7.710 141.566   1235
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 17.75 %
    Favored  : 77.42 %
  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 (0.25), residues: 1126
  helix:  1.00 (0.19), residues: 740
  sheet:  None (None), residues: 0
  loop : -1.16 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 128 
 HIS   0.003   0.001   HIS E 372 
 PHE   0.019   0.001   PHE E 454 
 TYR   0.017   0.001   TYR E 340 
 ARG   0.009   0.001   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03868 (  527)
  hydrogen bonds       : angle       4.26377 ( 1572)
  covalent geometry    : bond        0.00270 ( 9349)
  covalent geometry    : angle       0.56267 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 142
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8124 (pptt) cc_final: 0.7890 (pptt)
REVERT: A  271 TYR cc_start: 0.8520 (m-80) cc_final: 0.8305 (m-80)
REVERT: A  391 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7487 (m-80)
REVERT: A  439 LYS cc_start: 0.8689 (mttt) cc_final: 0.8344 (mtpm)
REVERT: A  585 TRP cc_start: 0.7012 (m100) cc_final: 0.6593 (m-10)
REVERT: A  595 GLU cc_start: 0.7685 (mp0) cc_final: 0.7422 (mp0)
REVERT: E  100 LEU cc_start: 0.8316 (tt) cc_final: 0.7294 (mm)
REVERT: E  112 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7831 (ttp)
REVERT: E  119 TYR cc_start: 0.6931 (t80) cc_final: 0.6480 (t80)
REVERT: E  120 ASN cc_start: 0.8246 (m110) cc_final: 0.7951 (m110)
REVERT: E  242 MET cc_start: 0.7432 (mtm) cc_final: 0.7122 (mtt)
REVERT: E  337 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.6400 (p0)
REVERT: E  340 TYR cc_start: 0.6947 (t80) cc_final: 0.6727 (t80)
REVERT: E  425 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7898 (tm-30)
REVERT: E  438 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8124 (mm)
REVERT: E  479 THR cc_start: 0.6596 (m) cc_final: 0.5965 (t)
REVERT: E  508 MET cc_start: 0.5875 (ttm) cc_final: 0.5583 (ttm)
REVERT: E  600 LEU cc_start: 0.7436 (mm) cc_final: 0.6990 (mp)
REVERT: E  603 GLN cc_start: 0.6922 (mt0) cc_final: 0.6674 (mp10)
  outliers start: 46
  outliers final: 16
  residues processed: 171
  average time/residue: 0.6935
  time to fit residues: 132.8268
Evaluate side-chains
  142 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  112 MET
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  180 TRP
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  296 HIS
Chi-restraints excluded: chain E residue  337 ASN
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  566 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0770
   chunk 81 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 90 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.7744

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 GLN
A 236 GLN
** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.164649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.131834 restraints weight = 12460.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 1.97
r_work: 0.3526 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9349  Z= 0.192
  Angle     :  0.640  13.529  12757  Z= 0.321
  Chirality :  0.042   0.148   1418
  Planarity :  0.004   0.033   1554
  Dihedral  :  7.754 141.298   1231
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 17.86 %
    Favored  : 77.21 %
  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:  0.44 (0.26), residues: 1126
  helix:  0.85 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.71 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  80 
 HIS   0.006   0.001   HIS E 370 
 PHE   0.024   0.002   PHE A 362 
 TYR   0.021   0.002   TYR A 340 
 ARG   0.006   0.001   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05101 (  527)
  hydrogen bonds       : angle       4.47123 ( 1572)
  covalent geometry    : bond        0.00452 ( 9349)
  covalent geometry    : angle       0.64042 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 125
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8067 (pptt) cc_final: 0.7750 (pptt)
REVERT: A  410 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.9033 (m)
REVERT: A  439 LYS cc_start: 0.8744 (mttt) cc_final: 0.8350 (mtpm)
REVERT: A  581 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7881 (tm-30)
REVERT: A  585 TRP cc_start: 0.7197 (m100) cc_final: 0.6645 (m-10)
REVERT: A  595 GLU cc_start: 0.7927 (mp0) cc_final: 0.7642 (mp0)
REVERT: A  597 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7807 (mt-10)
REVERT: E  100 LEU cc_start: 0.8571 (tt) cc_final: 0.7512 (mm)
REVERT: E  119 TYR cc_start: 0.7026 (t80) cc_final: 0.6416 (t80)
REVERT: E  120 ASN cc_start: 0.8130 (m110) cc_final: 0.7878 (m110)
REVERT: E  242 MET cc_start: 0.7572 (mtm) cc_final: 0.7276 (mtt)
REVERT: E  254 LYS cc_start: 0.7675 (tptm) cc_final: 0.7136 (tppt)
REVERT: E  257 LYS cc_start: 0.5940 (OUTLIER) cc_final: 0.5374 (mmmt)
REVERT: E  438 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8152 (mm)
REVERT: E  603 GLN cc_start: 0.6893 (mt0) cc_final: 0.6686 (mp10)
  outliers start: 47
  outliers final: 16
  residues processed: 159
  average time/residue: 0.8710
  time to fit residues: 152.6188
Evaluate side-chains
  133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  168 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  581 GLN
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  534 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   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  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 598 HIS ** 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 = 0.4084 r_free = 0.4084 target = 0.168593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.135546 restraints weight = 12428.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 1.97
r_work: 0.3569 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3441 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9349  Z= 0.125
  Angle     :  0.582  15.426  12757  Z= 0.282
  Chirality :  0.038   0.129   1418
  Planarity :  0.003   0.029   1554
  Dihedral  :  7.475 140.772   1228
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.96 %
    Favored  : 76.26 %
  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:  0.70 (0.26), residues: 1126
  helix:  1.13 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.80 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  80 
 HIS   0.008   0.001   HIS E 370 
 PHE   0.018   0.001   PHE A 362 
 TYR   0.016   0.001   TYR A 575 
 ARG   0.005   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04169 (  527)
  hydrogen bonds       : angle       4.33693 ( 1572)
  covalent geometry    : bond        0.00286 ( 9349)
  covalent geometry    : angle       0.58183 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8032 (pptt) cc_final: 0.7641 (pptt)
REVERT: A  439 LYS cc_start: 0.8746 (mttt) cc_final: 0.8366 (mtpm)
REVERT: A  585 TRP cc_start: 0.7173 (m100) cc_final: 0.6702 (m-10)
REVERT: A  595 GLU cc_start: 0.7803 (mp0) cc_final: 0.7565 (mp0)
REVERT: E  100 LEU cc_start: 0.8550 (tt) cc_final: 0.7422 (mm)
REVERT: E  119 TYR cc_start: 0.7032 (t80) cc_final: 0.6379 (t80)
REVERT: E  120 ASN cc_start: 0.8017 (m110) cc_final: 0.7531 (m110)
REVERT: E  242 MET cc_start: 0.7518 (mtm) cc_final: 0.7252 (mtt)
REVERT: E  254 LYS cc_start: 0.7658 (tptm) cc_final: 0.7112 (tppt)
REVERT: E  257 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5384 (mmmt)
REVERT: E  438 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8119 (mm)
REVERT: E  595 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7379 (mp0)
REVERT: E  600 LEU cc_start: 0.7280 (mm) cc_final: 0.6808 (mp)
REVERT: E  603 GLN cc_start: 0.6898 (mt0) cc_final: 0.6632 (mp10)
  outliers start: 36
  outliers final: 17
  residues processed: 148
  average time/residue: 0.7064
  time to fit residues: 116.8845
Evaluate side-chains
  133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  595 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 14 optimal weight:   20.0000
   chunk 94 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.172344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.137285 restraints weight = 12179.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.18
r_work: 0.3679 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.4700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9349  Z= 0.173
  Angle     :  0.627  16.211  12757  Z= 0.309
  Chirality :  0.041   0.175   1418
  Planarity :  0.004   0.029   1554
  Dihedral  :  7.610 140.542   1227
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 19.75 %
    Favored  : 76.16 %
  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:  0.65 (0.26), residues: 1126
  helix:  1.06 (0.19), residues: 747
  sheet:  None (None), residues: 0
  loop : -0.75 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E  80 
 HIS   0.010   0.001   HIS E 370 
 PHE   0.022   0.002   PHE A 362 
 TYR   0.018   0.002   TYR A 340 
 ARG   0.005   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04757 (  527)
  hydrogen bonds       : angle       4.42822 ( 1572)
  covalent geometry    : bond        0.00411 ( 9349)
  covalent geometry    : angle       0.62698 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 118
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8038 (pptt) cc_final: 0.7623 (pptt)
REVERT: A  297 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8242 (pp)
REVERT: A  439 LYS cc_start: 0.8780 (mttt) cc_final: 0.8412 (mtpm)
REVERT: A  509 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7049 (mpp)
REVERT: A  581 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8000 (tm-30)
REVERT: A  585 TRP cc_start: 0.7227 (m100) cc_final: 0.6716 (m-10)
REVERT: A  595 GLU cc_start: 0.7977 (mp0) cc_final: 0.7685 (mp0)
REVERT: A  596 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8402 (m-40)
REVERT: E  119 TYR cc_start: 0.6970 (t80) cc_final: 0.6480 (t80)
REVERT: E  120 ASN cc_start: 0.8024 (m110) cc_final: 0.7765 (m110)
REVERT: E  242 MET cc_start: 0.7648 (mtm) cc_final: 0.7327 (mtt)
REVERT: E  254 LYS cc_start: 0.7714 (tptm) cc_final: 0.7162 (tppt)
REVERT: E  257 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5264 (mtpm)
REVERT: E  436 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8358 (mp10)
REVERT: E  438 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8152 (mm)
REVERT: E  600 LEU cc_start: 0.7326 (mm) cc_final: 0.6826 (mp)
REVERT: E  603 GLN cc_start: 0.6966 (mt0) cc_final: 0.6675 (mp10)
  outliers start: 39
  outliers final: 18
  residues processed: 147
  average time/residue: 0.8272
  time to fit residues: 135.9404
Evaluate side-chains
  134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  581 GLN
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  436 GLN
Chi-restraints excluded: chain E residue  438 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 110 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 598 HIS ** 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 = 0.4226 r_free = 0.4226 target = 0.173863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.139225 restraints weight = 12302.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 2.19
r_work: 0.3717 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3581 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.4723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9349  Z= 0.135
  Angle     :  0.606  17.962  12757  Z= 0.293
  Chirality :  0.039   0.152   1418
  Planarity :  0.004   0.057   1554
  Dihedral  :  7.506 140.372   1227
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 20.38 %
    Favored  : 75.53 %
  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:  0.79 (0.26), residues: 1126
  helix:  1.20 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.75 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E  80 
 HIS   0.004   0.001   HIS E 598 
 PHE   0.020   0.001   PHE A 362 
 TYR   0.014   0.001   TYR A 575 
 ARG   0.004   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04311 (  527)
  hydrogen bonds       : angle       4.37193 ( 1572)
  covalent geometry    : bond        0.00311 ( 9349)
  covalent geometry    : angle       0.60632 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 110
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8008 (pptt) cc_final: 0.7553 (pptt)
REVERT: A  439 LYS cc_start: 0.8779 (mttt) cc_final: 0.8417 (mtpm)
REVERT: A  585 TRP cc_start: 0.7197 (m100) cc_final: 0.6706 (m-10)
REVERT: A  595 GLU cc_start: 0.7921 (mp0) cc_final: 0.7655 (mp0)
REVERT: E  119 TYR cc_start: 0.6949 (t80) cc_final: 0.6497 (t80)
REVERT: E  120 ASN cc_start: 0.7999 (m110) cc_final: 0.7724 (m110)
REVERT: E  242 MET cc_start: 0.7608 (mtm) cc_final: 0.7337 (mtt)
REVERT: E  254 LYS cc_start: 0.7659 (tptm) cc_final: 0.7105 (tppt)
REVERT: E  257 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5295 (mtpm)
REVERT: E  350 ASN cc_start: 0.6265 (m110) cc_final: 0.6007 (m110)
REVERT: E  438 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8152 (mm)
REVERT: E  479 THR cc_start: 0.6837 (OUTLIER) cc_final: 0.6115 (t)
REVERT: E  584 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4749 (tt)
REVERT: E  600 LEU cc_start: 0.7324 (mm) cc_final: 0.6829 (mp)
REVERT: E  603 GLN cc_start: 0.6992 (mt0) cc_final: 0.6698 (mp10)
  outliers start: 39
  outliers final: 18
  residues processed: 140
  average time/residue: 0.7403
  time to fit residues: 115.3787
Evaluate side-chains
  127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  180 TRP
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  479 THR
Chi-restraints excluded: chain E residue  528 PHE
Chi-restraints excluded: chain E residue  584 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 46 optimal weight:    0.3980
   chunk 96 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 13 optimal weight:    0.4980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 370 HIS ** 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 = 0.4248 r_free = 0.4248 target = 0.176386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.145251 restraints weight = 12418.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 1.98
r_work: 0.3764 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9349  Z= 0.116
  Angle     :  0.597  17.970  12757  Z= 0.284
  Chirality :  0.038   0.201   1418
  Planarity :  0.003   0.045   1554
  Dihedral  :  7.403 140.420   1227
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.74 %
    Favored  : 75.11 %
  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:  0.94 (0.26), residues: 1126
  helix:  1.33 (0.19), residues: 747
  sheet:  None (None), residues: 0
  loop : -0.74 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E  80 
 HIS   0.004   0.001   HIS E 598 
 PHE   0.023   0.001   PHE E 275 
 TYR   0.019   0.001   TYR E 340 
 ARG   0.003   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  527)
  hydrogen bonds       : angle       4.28042 ( 1572)
  covalent geometry    : bond        0.00259 ( 9349)
  covalent geometry    : angle       0.59704 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7806 (pptt) cc_final: 0.7335 (pptt)
REVERT: A  439 LYS cc_start: 0.8726 (mttt) cc_final: 0.8362 (mtpm)
REVERT: A  509 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.6843 (mpp)
REVERT: A  585 TRP cc_start: 0.7166 (m100) cc_final: 0.6690 (m-10)
REVERT: A  595 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7524 (mp0)
REVERT: E  119 TYR cc_start: 0.6993 (t80) cc_final: 0.6538 (t80)
REVERT: E  120 ASN cc_start: 0.7923 (m110) cc_final: 0.7554 (m110)
REVERT: E  242 MET cc_start: 0.7592 (mtm) cc_final: 0.7264 (mtt)
REVERT: E  254 LYS cc_start: 0.7644 (tptm) cc_final: 0.7072 (tppt)
REVERT: E  257 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5411 (mmmt)
REVERT: E  438 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8101 (mm)
REVERT: E  479 THR cc_start: 0.6709 (OUTLIER) cc_final: 0.6412 (t)
REVERT: E  584 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4631 (tt)
REVERT: E  600 LEU cc_start: 0.7383 (mm) cc_final: 0.7107 (mp)
REVERT: E  612 GLN cc_start: 0.6717 (tm-30) cc_final: 0.6515 (mm-40)
  outliers start: 30
  outliers final: 18
  residues processed: 137
  average time/residue: 0.8032
  time to fit residues: 124.1335
Evaluate side-chains
  137 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  479 THR
Chi-restraints excluded: chain E residue  528 PHE
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  606 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0010
   chunk 21 optimal weight:    0.6980
   chunk 56 optimal weight:   20.0000
   chunk 81 optimal weight:    7.9990
   chunk 33 optimal weight:    0.2980
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 370 HIS ** 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 = 0.4181 r_free = 0.4181 target = 0.172942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.137882 restraints weight = 12155.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 2.24
r_work: 0.3667 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3529 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9349  Z= 0.115
  Angle     :  0.610  17.245  12757  Z= 0.286
  Chirality :  0.038   0.201   1418
  Planarity :  0.003   0.049   1554
  Dihedral  :  7.367 140.483   1227
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.06 %
    Favored  : 74.89 %
  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:  1.06 (0.26), residues: 1126
  helix:  1.40 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -0.65 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E  80 
 HIS   0.003   0.001   HIS A 441 
 PHE   0.018   0.001   PHE A 362 
 TYR   0.015   0.001   TYR A 575 
 ARG   0.003   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03868 (  527)
  hydrogen bonds       : angle       4.25354 ( 1572)
  covalent geometry    : bond        0.00254 ( 9349)
  covalent geometry    : angle       0.60954 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7806 (pptt) cc_final: 0.7335 (pptt)
REVERT: A  439 LYS cc_start: 0.8768 (mttt) cc_final: 0.8373 (mtpm)
REVERT: A  509 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.6934 (mpp)
REVERT: A  585 TRP cc_start: 0.7176 (m100) cc_final: 0.6626 (m-10)
REVERT: A  595 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7580 (mp0)
REVERT: E  119 TYR cc_start: 0.6995 (t80) cc_final: 0.6532 (t80)
REVERT: E  120 ASN cc_start: 0.7880 (m110) cc_final: 0.7667 (m110)
REVERT: E  242 MET cc_start: 0.7653 (mtm) cc_final: 0.7334 (mtt)
REVERT: E  254 LYS cc_start: 0.7656 (tptm) cc_final: 0.7212 (tppp)
REVERT: E  257 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5462 (mmmt)
REVERT: E  350 ASN cc_start: 0.6122 (m110) cc_final: 0.5836 (m110)
REVERT: E  438 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7970 (mm)
REVERT: E  479 THR cc_start: 0.6722 (OUTLIER) cc_final: 0.6436 (t)
REVERT: E  584 LEU cc_start: 0.4882 (OUTLIER) cc_final: 0.4507 (tt)
REVERT: E  600 LEU cc_start: 0.7349 (mm) cc_final: 0.7074 (mp)
  outliers start: 29
  outliers final: 14
  residues processed: 144
  average time/residue: 0.6970
  time to fit residues: 112.5718
Evaluate side-chains
  132 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  479 THR
Chi-restraints excluded: chain E residue  528 PHE
Chi-restraints excluded: chain E residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 111 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 84 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0270
   overall best weight:    0.6840

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

Flipped N/Q/H residues before XYZ refinement:
** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 370 HIS ** 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 = 0.4174 r_free = 0.4174 target = 0.172177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.136890 restraints weight = 12373.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.27
r_work: 0.3647 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.4778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9349  Z= 0.121
  Angle     :  0.624  17.496  12757  Z= 0.292
  Chirality :  0.038   0.148   1418
  Planarity :  0.003   0.043   1554
  Dihedral  :  7.367 140.496   1227
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.48 %
    Favored  : 75.00 %
  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:  1.08 (0.26), residues: 1126
  helix:  1.40 (0.19), residues: 751
  sheet:  None (None), residues: 0
  loop : -0.61 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E  80 
 HIS   0.003   0.000   HIS E 598 
 PHE   0.034   0.001   PHE A 275 
 TYR   0.019   0.001   TYR E 340 
 ARG   0.003   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03946 (  527)
  hydrogen bonds       : angle       4.24833 ( 1572)
  covalent geometry    : bond        0.00273 ( 9349)
  covalent geometry    : angle       0.62423 (12757)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7761 (pptt) cc_final: 0.7285 (pptt)
REVERT: A  439 LYS cc_start: 0.8771 (mttt) cc_final: 0.8388 (mtpm)
REVERT: A  509 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.6887 (mpp)
REVERT: A  585 TRP cc_start: 0.7182 (m100) cc_final: 0.6637 (m-10)
REVERT: A  595 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7582 (mp0)
REVERT: E  119 TYR cc_start: 0.6970 (t80) cc_final: 0.6550 (t80)
REVERT: E  120 ASN cc_start: 0.7956 (m110) cc_final: 0.7744 (m110)
REVERT: E  242 MET cc_start: 0.7682 (mtm) cc_final: 0.7357 (mtt)
REVERT: E  254 LYS cc_start: 0.7674 (tptm) cc_final: 0.7226 (tppp)
REVERT: E  257 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5432 (mmmt)
REVERT: E  350 ASN cc_start: 0.6119 (m110) cc_final: 0.5837 (m110)
REVERT: E  438 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7981 (mm)
REVERT: E  479 THR cc_start: 0.6716 (OUTLIER) cc_final: 0.6221 (t)
REVERT: E  584 LEU cc_start: 0.4944 (OUTLIER) cc_final: 0.4551 (tt)
REVERT: E  600 LEU cc_start: 0.7390 (mm) cc_final: 0.7086 (mp)
  outliers start: 24
  outliers final: 16
  residues processed: 131
  average time/residue: 0.6851
  time to fit residues: 100.6920
Evaluate side-chains
  135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain E residue  116 LEU
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  479 THR
Chi-restraints excluded: chain E residue  528 PHE
Chi-restraints excluded: chain E residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 108 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.169934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.134081 restraints weight = 12289.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.25
r_work: 0.3611 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.4899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9349  Z= 0.142
  Angle     :  0.637  16.683  12757  Z= 0.303
  Chirality :  0.041   0.460   1418
  Planarity :  0.004   0.039   1554
  Dihedral  :  7.437 140.481   1227
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 22.16 %
    Favored  : 75.00 %
  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:  1.05 (0.26), residues: 1126
  helix:  1.33 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -0.52 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E  80 
 HIS   0.002   0.001   HIS A 222 
 PHE   0.020   0.001   PHE A 362 
 TYR   0.015   0.001   TYR A 340 
 ARG   0.003   0.000   ARG A 512 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04359 (  527)
  hydrogen bonds       : angle       4.30643 ( 1572)
  covalent geometry    : bond        0.00328 ( 9349)
  covalent geometry    : angle       0.63695 (12757)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6817.88 seconds
wall clock time: 119 minutes 53.96 seconds (7193.96 seconds total)