Starting phenix.real_space_refine
on Sat Aug 23 01:39:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y93_39068/08_2025/8y93_39068.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y93_39068/08_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_39068/08_2025/8y93_39068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y93_39068/08_2025/8y93_39068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y93_39068/08_2025/8y93_39068.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y93_39068/08_2025/8y93_39068.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.055
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.49, per 1000 atoms: 0.27
  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: 1.04
  Conformation dependent library (CDL) restraints added in 371.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.30
  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: 1.61

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.20 -     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:             3.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.760
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.680
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG E 216 
 TYR   0.007   0.001   TYR A 340 
 PHE   0.011   0.001   PHE A 409 
 TRP   0.015   0.001   TRP E 128 
 HIS   0.001   0.000   HIS A 280 

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

*********************** 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  : 0.337 
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: 0.4091
  time to fit residues: 124.9499
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  : 0.316 
-------------------------------------------------------------------------------
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 108 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    7.9990
   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  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 153 ASN
A 234 GLN
A 236 GLN
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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.178191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.146252 restraints weight = 12454.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 2.09
r_work: 0.3711 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9349  Z= 0.152
  Angle     :  0.604  10.600  12757  Z= 0.304
  Chirality :  0.041   0.172   1418
  Planarity :  0.004   0.032   1554
  Dihedral  :  8.126 141.241   1242
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 17.02 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.25), residues: 1126
  helix:  0.43 (0.19), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.43 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 604 
 TYR   0.018   0.001   TYR A 111 
 PHE   0.020   0.002   PHE A 362 
 TRP   0.017   0.001   TRP A 128 
 HIS   0.005   0.001   HIS E 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9349)
  covalent geometry    : angle       0.60416 (12757)
  hydrogen bonds       : bond        0.04223 (  527)
  hydrogen bonds       : angle       4.51241 ( 1572)

*********************** 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
  210 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 163
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  439 LYS cc_start: 0.8814 (mttt) cc_final: 0.8434 (mtpm)
REVERT: A  585 TRP cc_start: 0.7189 (m100) cc_final: 0.6671 (m-10)
REVERT: A  595 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7538 (mp0)
REVERT: E  100 LEU cc_start: 0.8370 (tt) cc_final: 0.7279 (mm)
REVERT: E  119 TYR cc_start: 0.6941 (t80) cc_final: 0.6548 (t80)
REVERT: E  120 ASN cc_start: 0.8347 (m110) cc_final: 0.8087 (m-40)
REVERT: E  121 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7843 (mpt90)
REVERT: E  242 MET cc_start: 0.7604 (mtm) cc_final: 0.7347 (mtt)
REVERT: E  254 LYS cc_start: 0.7691 (tptm) cc_final: 0.7278 (tppp)
REVERT: E  350 ASN cc_start: 0.6097 (m110) cc_final: 0.5759 (m110)
REVERT: E  436 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8253 (mp10)
REVERT: E  438 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8142 (mm)
REVERT: E  595 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7333 (mp0)
REVERT: E  603 GLN cc_start: 0.6935 (mt0) cc_final: 0.6690 (mp10)
  outliers start: 47
  outliers final: 17
  residues processed: 193
  average time/residue: 0.3935
  time to fit residues: 83.8484
Evaluate side-chains
  149 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  159 SER
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  420 SER
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  565 SER
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
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  595 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 99 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 88 optimal weight:    9.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.178747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.144295 restraints weight = 12145.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 2.23
r_work: 0.3717 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3578 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9349  Z= 0.127
  Angle     :  0.572  16.226  12757  Z= 0.279
  Chirality :  0.039   0.136   1418
  Planarity :  0.004   0.029   1554
  Dihedral  :  7.615 141.471   1233
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 17.75 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.25), residues: 1126
  helix:  0.94 (0.19), residues: 739
  sheet:  None (None), residues: 0
  loop : -1.10 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 512 
 TYR   0.018   0.001   TYR E 340 
 PHE   0.019   0.001   PHE E 454 
 TRP   0.010   0.001   TRP A 128 
 HIS   0.007   0.001   HIS E 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9349)
  covalent geometry    : angle       0.57171 (12757)
  hydrogen bonds       : bond        0.04035 (  527)
  hydrogen bonds       : angle       4.34213 ( 1572)

*********************** 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
  179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 134
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8224 (pptt) cc_final: 0.7960 (pptt)
REVERT: A  391 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7708 (m-80)
REVERT: A  439 LYS cc_start: 0.8795 (mttt) cc_final: 0.8419 (mtpm)
REVERT: A  585 TRP cc_start: 0.7176 (m100) cc_final: 0.6632 (m-10)
REVERT: A  595 GLU cc_start: 0.7828 (mp0) cc_final: 0.7571 (mp0)
REVERT: A  597 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7697 (mt-10)
REVERT: E  100 LEU cc_start: 0.8427 (tt) cc_final: 0.7395 (mm)
REVERT: E  119 TYR cc_start: 0.6956 (t80) cc_final: 0.6514 (t80)
REVERT: E  120 ASN cc_start: 0.8216 (m110) cc_final: 0.7891 (m110)
REVERT: E  242 MET cc_start: 0.7579 (mtm) cc_final: 0.7295 (mtt)
REVERT: E  254 LYS cc_start: 0.7745 (tptm) cc_final: 0.7376 (tppp)
REVERT: E  337 ASN cc_start: 0.6991 (OUTLIER) cc_final: 0.6446 (p0)
REVERT: E  350 ASN cc_start: 0.6107 (m110) cc_final: 0.5784 (m110)
REVERT: E  438 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8125 (mm)
REVERT: E  479 THR cc_start: 0.6788 (m) cc_final: 0.6072 (t)
REVERT: E  600 LEU cc_start: 0.7353 (mm) cc_final: 0.6908 (mp)
REVERT: E  603 GLN cc_start: 0.6888 (mt0) cc_final: 0.6627 (mp10)
  outliers start: 45
  outliers final: 16
  residues processed: 162
  average time/residue: 0.3592
  time to fit residues: 65.0525
Evaluate side-chains
  139 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  390 LEU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  490 ILE
Chi-restraints excluded: chain A residue  565 SER
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  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  359 PHE
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  486 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 109 optimal weight:   10.0000
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 87 optimal weight:    7.9990
   chunk 105 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.166249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.133163 restraints weight = 12611.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.98
r_work: 0.3540 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9349  Z= 0.169
  Angle     :  0.602  14.821  12757  Z= 0.300
  Chirality :  0.040   0.140   1418
  Planarity :  0.004   0.032   1554
  Dihedral  :  7.687 141.218   1232
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.49 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.26), residues: 1126
  helix:  0.98 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.92 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 512 
 TYR   0.018   0.001   TYR A 340 
 PHE   0.023   0.002   PHE A 362 
 TRP   0.014   0.001   TRP A  80 
 HIS   0.007   0.001   HIS E 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9349)
  covalent geometry    : angle       0.60184 (12757)
  hydrogen bonds       : bond        0.04722 (  527)
  hydrogen bonds       : angle       4.41080 ( 1572)

*********************** 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
  171 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 126
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8117 (pptt) cc_final: 0.7816 (pptt)
REVERT: A  410 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9038 (m)
REVERT: A  439 LYS cc_start: 0.8775 (mttt) cc_final: 0.8383 (mtpm)
REVERT: A  581 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7884 (tm-30)
REVERT: A  585 TRP cc_start: 0.7183 (m100) cc_final: 0.6638 (m-10)
REVERT: A  595 GLU cc_start: 0.7888 (mp0) cc_final: 0.7596 (mp0)
REVERT: A  597 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7784 (mt-10)
REVERT: E  100 LEU cc_start: 0.8555 (tt) cc_final: 0.7505 (mm)
REVERT: E  119 TYR cc_start: 0.7057 (t80) cc_final: 0.6567 (t80)
REVERT: E  120 ASN cc_start: 0.8125 (m110) cc_final: 0.7808 (m110)
REVERT: E  190 LEU cc_start: 0.6546 (tp) cc_final: 0.6264 (pt)
REVERT: E  242 MET cc_start: 0.7570 (mtm) cc_final: 0.7280 (mtt)
REVERT: E  254 LYS cc_start: 0.7789 (tptm) cc_final: 0.7214 (tppt)
REVERT: E  257 LYS cc_start: 0.5934 (OUTLIER) cc_final: 0.5373 (mmmt)
REVERT: E  350 ASN cc_start: 0.6291 (m110) cc_final: 0.6067 (m110)
REVERT: E  370 HIS cc_start: 0.5186 (OUTLIER) cc_final: 0.4962 (p90)
REVERT: E  438 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8114 (mm)
REVERT: E  461 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7854 (pp)
REVERT: E  603 GLN cc_start: 0.6877 (mt0) cc_final: 0.6647 (mp10)
  outliers start: 45
  outliers final: 17
  residues processed: 160
  average time/residue: 0.3649
  time to fit residues: 65.1606
Evaluate side-chains
  142 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  265 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  410 VAL
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  596 ASN
Chi-restraints excluded: chain A residue  597 GLU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  112 MET
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  337 ASN
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  370 HIS
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  461 ILE
Chi-restraints excluded: chain E residue  566 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 110 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 70 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  54 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 = 0.4055 r_free = 0.4055 target = 0.166303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.133204 restraints weight = 12498.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 1.96
r_work: 0.3515 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9349  Z= 0.152
  Angle     :  0.593  14.433  12757  Z= 0.291
  Chirality :  0.040   0.194   1418
  Planarity :  0.004   0.030   1554
  Dihedral  :  7.569 140.757   1229
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 19.33 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.26), residues: 1126
  helix:  1.10 (0.19), residues: 741
  sheet:  None (None), residues: 0
  loop : -0.76 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 512 
 TYR   0.018   0.001   TYR E 340 
 PHE   0.021   0.001   PHE A 362 
 TRP   0.014   0.001   TRP E  80 
 HIS   0.006   0.001   HIS E 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9349)
  covalent geometry    : angle       0.59340 (12757)
  hydrogen bonds       : bond        0.04436 (  527)
  hydrogen bonds       : angle       4.38548 ( 1572)

*********************** 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
  161 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 117
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8101 (pptt) cc_final: 0.7688 (pptt)
REVERT: A  297 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8202 (pp)
REVERT: A  439 LYS cc_start: 0.8772 (mttt) cc_final: 0.8395 (mtpm)
REVERT: A  581 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7993 (tm-30)
REVERT: A  585 TRP cc_start: 0.7198 (m100) cc_final: 0.6715 (m-10)
REVERT: A  595 GLU cc_start: 0.7873 (mp0) cc_final: 0.7619 (mp0)
REVERT: E  119 TYR cc_start: 0.7012 (t80) cc_final: 0.6523 (t80)
REVERT: E  120 ASN cc_start: 0.7984 (m110) cc_final: 0.7733 (m110)
REVERT: E  242 MET cc_start: 0.7570 (mtm) cc_final: 0.7280 (mtt)
REVERT: E  254 LYS cc_start: 0.7738 (tptm) cc_final: 0.7204 (tppt)
REVERT: E  257 LYS cc_start: 0.5883 (OUTLIER) cc_final: 0.5342 (mmmt)
REVERT: E  438 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8145 (mm)
REVERT: E  461 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7924 (pp)
REVERT: E  600 LEU cc_start: 0.7284 (mm) cc_final: 0.6796 (mp)
REVERT: E  603 GLN cc_start: 0.6944 (mt0) cc_final: 0.6659 (mp10)
  outliers start: 44
  outliers final: 18
  residues processed: 152
  average time/residue: 0.3582
  time to fit residues: 60.6669
Evaluate side-chains
  133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
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  265 ILE
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  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  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  421 MET
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  461 ILE
Chi-restraints excluded: chain E residue  528 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 88 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4236 r_free = 0.4236 target = 0.175206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.140772 restraints weight = 12271.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 2.18
r_work: 0.3727 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3597 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.4534

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= 0.123
  Angle     :  0.583  16.350  12757  Z= 0.282
  Chirality :  0.039   0.167   1418
  Planarity :  0.004   0.053   1554
  Dihedral  :  7.596 140.559   1229
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.17 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.26), residues: 1126
  helix:  1.27 (0.19), residues: 740
  sheet:  None (None), residues: 0
  loop : -0.77 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 512 
 TYR   0.011   0.001   TYR A 340 
 PHE   0.019   0.001   PHE A 362 
 TRP   0.020   0.001   TRP E  80 
 HIS   0.005   0.001   HIS E 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9349)
  covalent geometry    : angle       0.58275 (12757)
  hydrogen bonds       : bond        0.04074 (  527)
  hydrogen bonds       : angle       4.32676 ( 1572)

*********************** 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
  158 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 120
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8002 (pptt) cc_final: 0.7582 (pptt)
REVERT: A  297 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8244 (pp)
REVERT: A  439 LYS cc_start: 0.8760 (mttt) cc_final: 0.8386 (mtpm)
REVERT: A  585 TRP cc_start: 0.7177 (m100) cc_final: 0.6709 (m-10)
REVERT: A  595 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7604 (mp0)
REVERT: E  112 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8066 (ttp)
REVERT: E  119 TYR cc_start: 0.6946 (t80) cc_final: 0.6453 (t80)
REVERT: E  120 ASN cc_start: 0.7947 (m110) cc_final: 0.7698 (m110)
REVERT: E  242 MET cc_start: 0.7608 (mtm) cc_final: 0.7291 (mtt)
REVERT: E  254 LYS cc_start: 0.7725 (tptm) cc_final: 0.7194 (tppt)
REVERT: E  257 LYS cc_start: 0.5865 (OUTLIER) cc_final: 0.5230 (mtpm)
REVERT: E  370 HIS cc_start: 0.4981 (OUTLIER) cc_final: 0.4771 (p90)
REVERT: E  438 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8154 (mm)
REVERT: E  461 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7924 (pp)
REVERT: E  600 LEU cc_start: 0.7370 (mm) cc_final: 0.6882 (mp)
REVERT: E  603 GLN cc_start: 0.6973 (mt0) cc_final: 0.6673 (mp10)
  outliers start: 38
  outliers final: 15
  residues processed: 147
  average time/residue: 0.3206
  time to fit residues: 52.5880
Evaluate side-chains
  131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
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  297 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  595 GLU
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  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  370 HIS
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  461 ILE
Chi-restraints excluded: chain E residue  528 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 76 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 57 optimal weight:    9.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4243 r_free = 0.4243 target = 0.176431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.140124 restraints weight = 12411.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 2.29
r_work: 0.3724 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3588 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.4592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9349  Z= 0.124
  Angle     :  0.602  17.819  12757  Z= 0.286
  Chirality :  0.039   0.225   1418
  Planarity :  0.003   0.040   1554
  Dihedral  :  7.556 140.507   1229
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 20.59 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.26), residues: 1126
  helix:  1.34 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.80 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 512 
 TYR   0.018   0.001   TYR E 340 
 PHE   0.019   0.001   PHE A 362 
 TRP   0.020   0.001   TRP E  80 
 HIS   0.004   0.001   HIS E 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9349)
  covalent geometry    : angle       0.60184 (12757)
  hydrogen bonds       : bond        0.04045 (  527)
  hydrogen bonds       : angle       4.29704 ( 1572)

*********************** 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
  152 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 113
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7917 (pptt) cc_final: 0.7455 (pptt)
REVERT: A  297 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8197 (pp)
REVERT: A  439 LYS cc_start: 0.8765 (mttt) cc_final: 0.8392 (mtpm)
REVERT: A  581 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7947 (tm-30)
REVERT: A  585 TRP cc_start: 0.7188 (m100) cc_final: 0.6672 (m-10)
REVERT: A  595 GLU cc_start: 0.7863 (mp0) cc_final: 0.7563 (mp0)
REVERT: E  119 TYR cc_start: 0.6962 (t80) cc_final: 0.6492 (t80)
REVERT: E  120 ASN cc_start: 0.8015 (m110) cc_final: 0.7692 (m110)
REVERT: E  242 MET cc_start: 0.7623 (mtm) cc_final: 0.7302 (mtt)
REVERT: E  254 LYS cc_start: 0.7712 (tptm) cc_final: 0.7152 (tppt)
REVERT: E  257 LYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5338 (mtpm)
REVERT: E  438 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8113 (mm)
REVERT: E  461 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7925 (pp)
REVERT: E  479 THR cc_start: 0.6800 (m) cc_final: 0.6103 (t)
REVERT: E  584 LEU cc_start: 0.4947 (OUTLIER) cc_final: 0.4594 (tt)
REVERT: E  598 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.5320 (m-70)
REVERT: E  600 LEU cc_start: 0.7416 (mm) cc_final: 0.6951 (mp)
REVERT: E  603 GLN cc_start: 0.6985 (mt0) cc_final: 0.6658 (mp10)
  outliers start: 39
  outliers final: 19
  residues processed: 143
  average time/residue: 0.3222
  time to fit residues: 51.8479
Evaluate side-chains
  135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
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  297 ILE
Chi-restraints excluded: chain A residue  345 LEU
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  611 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  112 MET
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  359 PHE
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  461 ILE
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  598 HIS
Chi-restraints excluded: chain E residue  606 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0770
   chunk 23 optimal weight:    6.9990
   chunk 104 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8342

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.175384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.141093 restraints weight = 12263.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 2.18
r_work: 0.3732 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.4682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9349  Z= 0.127
  Angle     :  0.613  18.314  12757  Z= 0.291
  Chirality :  0.039   0.181   1418
  Planarity :  0.003   0.037   1554
  Dihedral  :  7.538 140.476   1229
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.22 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.26), residues: 1126
  helix:  1.35 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.74 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 512 
 TYR   0.012   0.001   TYR A 340 
 PHE   0.025   0.001   PHE E 275 
 TRP   0.021   0.001   TRP E  80 
 HIS   0.007   0.001   HIS E 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9349)
  covalent geometry    : angle       0.61313 (12757)
  hydrogen bonds       : bond        0.04125 (  527)
  hydrogen bonds       : angle       4.31187 ( 1572)

*********************** 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
  155 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7847 (pptt) cc_final: 0.7382 (pptt)
REVERT: A  297 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8230 (pp)
REVERT: A  439 LYS cc_start: 0.8748 (mttt) cc_final: 0.8386 (mtpm)
REVERT: A  581 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7935 (tm-30)
REVERT: A  585 TRP cc_start: 0.7212 (m100) cc_final: 0.6694 (m-10)
REVERT: A  595 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7541 (mp0)
REVERT: E  119 TYR cc_start: 0.7023 (t80) cc_final: 0.6583 (t80)
REVERT: E  120 ASN cc_start: 0.7951 (m110) cc_final: 0.7750 (m110)
REVERT: E  242 MET cc_start: 0.7632 (mtm) cc_final: 0.7295 (mtt)
REVERT: E  254 LYS cc_start: 0.7737 (tptm) cc_final: 0.7181 (tppt)
REVERT: E  257 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5347 (mtpm)
REVERT: E  408 PHE cc_start: 0.7991 (t80) cc_final: 0.7711 (t80)
REVERT: E  412 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7622 (mp)
REVERT: E  438 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8116 (mm)
REVERT: E  461 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7929 (pp)
REVERT: E  479 THR cc_start: 0.6690 (m) cc_final: 0.6134 (t)
REVERT: E  584 LEU cc_start: 0.4911 (OUTLIER) cc_final: 0.4538 (tt)
REVERT: E  598 HIS cc_start: 0.6146 (OUTLIER) cc_final: 0.5354 (m-70)
REVERT: E  600 LEU cc_start: 0.7429 (mm) cc_final: 0.7139 (mp)
REVERT: E  612 GLN cc_start: 0.6869 (tm-30) cc_final: 0.6498 (tp40)
  outliers start: 39
  outliers final: 19
  residues processed: 146
  average time/residue: 0.3314
  time to fit residues: 53.9906
Evaluate side-chains
  139 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
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  265 ILE
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  345 LEU
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  581 GLN
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  112 MET
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  412 LEU
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  461 ILE
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  598 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 105 optimal weight:    0.0470
   chunk 31 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0370
   chunk 79 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0020
   chunk 80 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.2564

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.180517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.145146 restraints weight = 12458.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 2.30
r_work: 0.3788 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.4581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9349  Z= 0.106
  Angle     :  0.603  16.806  12757  Z= 0.281
  Chirality :  0.038   0.147   1418
  Planarity :  0.003   0.048   1554
  Dihedral  :  7.405 140.390   1229
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.58 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.26), residues: 1126
  helix:  1.49 (0.19), residues: 743
  sheet:  None (None), residues: 0
  loop : -0.74 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 512 
 TYR   0.018   0.001   TYR E 340 
 PHE   0.017   0.001   PHE A 362 
 TRP   0.026   0.001   TRP E  80 
 HIS   0.003   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9349)
  covalent geometry    : angle       0.60271 (12757)
  hydrogen bonds       : bond        0.03490 (  527)
  hydrogen bonds       : angle       4.23282 ( 1572)

*********************** 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
  155 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7696 (pptt) cc_final: 0.6607 (ptmt)
REVERT: A  190 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6992 (pt)
REVERT: A  439 LYS cc_start: 0.8706 (mttt) cc_final: 0.8340 (mtpm)
REVERT: A  585 TRP cc_start: 0.7114 (m100) cc_final: 0.6606 (m-10)
REVERT: A  595 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7465 (mp0)
REVERT: E  112 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7972 (ttp)
REVERT: E  119 TYR cc_start: 0.6936 (t80) cc_final: 0.6491 (t80)
REVERT: E  120 ASN cc_start: 0.7941 (m110) cc_final: 0.7630 (m110)
REVERT: E  242 MET cc_start: 0.7649 (mtm) cc_final: 0.7335 (mtt)
REVERT: E  254 LYS cc_start: 0.7718 (tptm) cc_final: 0.7226 (tppp)
REVERT: E  257 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5460 (mmmt)
REVERT: E  350 ASN cc_start: 0.6020 (m110) cc_final: 0.5741 (m110)
REVERT: E  438 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8056 (mm)
REVERT: E  461 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7912 (pp)
REVERT: E  479 THR cc_start: 0.6417 (m) cc_final: 0.6003 (t)
REVERT: E  584 LEU cc_start: 0.4876 (OUTLIER) cc_final: 0.4532 (tt)
REVERT: E  600 LEU cc_start: 0.7473 (mm) cc_final: 0.7163 (mp)
  outliers start: 28
  outliers final: 14
  residues processed: 147
  average time/residue: 0.3365
  time to fit residues: 55.3393
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  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
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  230 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  595 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain E residue  112 MET
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  205 TYR
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  461 ILE
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  606 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 95 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 76 optimal weight:    0.4980
   chunk 104 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.178125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.142385 restraints weight = 12407.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 2.30
r_work: 0.3759 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.4724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9349  Z= 0.121
  Angle     :  0.635  17.655  12757  Z= 0.296
  Chirality :  0.038   0.157   1418
  Planarity :  0.004   0.041   1554
  Dihedral  :  7.456 140.593   1229
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 23.95 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.26), residues: 1126
  helix:  1.46 (0.19), residues: 747
  sheet:  None (None), residues: 0
  loop : -0.62 (0.34), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 442 
 TYR   0.011   0.001   TYR A 249 
 PHE   0.034   0.001   PHE A 275 
 TRP   0.022   0.001   TRP E  80 
 HIS   0.006   0.001   HIS E 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9349)
  covalent geometry    : angle       0.63468 (12757)
  hydrogen bonds       : bond        0.03878 (  527)
  hydrogen bonds       : angle       4.22393 ( 1572)

********************** 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
  137 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7658 (pptt) cc_final: 0.6592 (ptmt)
REVERT: A  439 LYS cc_start: 0.8722 (mttt) cc_final: 0.8369 (mtpm)
REVERT: A  585 TRP cc_start: 0.7169 (m100) cc_final: 0.6656 (m-10)
REVERT: A  595 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7463 (mp0)
REVERT: E  112 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7990 (ttp)
REVERT: E  119 TYR cc_start: 0.6960 (t80) cc_final: 0.6497 (t80)
REVERT: E  120 ASN cc_start: 0.7946 (m110) cc_final: 0.7695 (m110)
REVERT: E  242 MET cc_start: 0.7676 (mtm) cc_final: 0.7343 (mtt)
REVERT: E  254 LYS cc_start: 0.7681 (tptm) cc_final: 0.7218 (tppp)
REVERT: E  329 PHE cc_start: 0.7193 (m-10) cc_final: 0.6943 (m-10)
REVERT: E  350 ASN cc_start: 0.6127 (m110) cc_final: 0.5855 (m110)
REVERT: E  393 GLU cc_start: 0.5874 (mm-30) cc_final: 0.5661 (mm-30)
REVERT: E  438 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8020 (mm)
REVERT: E  461 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7966 (pp)
REVERT: E  479 THR cc_start: 0.6431 (m) cc_final: 0.6120 (t)
REVERT: E  584 LEU cc_start: 0.4920 (OUTLIER) cc_final: 0.4544 (tt)
REVERT: E  600 LEU cc_start: 0.7436 (mm) cc_final: 0.7144 (mp)
  outliers start: 22
  outliers final: 14
  residues processed: 131
  average time/residue: 0.2788
  time to fit residues: 40.9875
Evaluate side-chains
  133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 VAL
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  230 ILE
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  595 GLU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain E residue  112 MET
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  205 TYR
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  461 ILE
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 23 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 101 optimal weight:   10.0000
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.4143 r_free = 0.4143 target = 0.169535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.133777 restraints weight = 12136.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 2.27
r_work: 0.3609 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.4882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9349  Z= 0.151
  Angle     :  0.656  16.677  12757  Z= 0.313
  Chirality :  0.042   0.460   1418
  Planarity :  0.004   0.038   1554
  Dihedral  :  7.577 140.548   1229
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 24.05 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1126
  helix:  1.31 (0.19), residues: 753
  sheet:  None (None), residues: 0
  loop : -0.48 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 442 
 TYR   0.017   0.001   TYR E 340 
 PHE   0.021   0.001   PHE A 362 
 TRP   0.020   0.001   TRP E  80 
 HIS   0.006   0.001   HIS E 370 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9349)
  covalent geometry    : angle       0.65559 (12757)
  hydrogen bonds       : bond        0.04497 (  527)
  hydrogen bonds       : angle       4.31624 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3056.70 seconds
wall clock time: 53 minutes 1.60 seconds (3181.60 seconds total)