Starting phenix.real_space_refine
on Thu Jan 16 03:01:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y93_39068/01_2025/8y93_39068.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y93_39068/01_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_39068/01_2025/8y93_39068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y93_39068/01_2025/8y93_39068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y93_39068/01_2025/8y93_39068.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y93_39068/01_2025/8y93_39068.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      1      4.86       5
     Na      1      4.78       5
     C    6072      2.51       5
     N    1413      2.21       5
     O    1528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9055
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "E"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4516
          Classifications: {'peptide': 565}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 544}
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 23
          Unusual residues: {' CL': 1, ' NA': 1, 'TP0': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.76, per 1000 atoms: 0.64
  Number of scatterers: 9055
  At special positions: 0
  Unit cell: (97.09, 85.41, 118.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      40     16.00
     Na      1     11.00
     O    1528      8.00
     N    1413      7.00
     C    6072      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.98
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 0 sheets defined
      72.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 74
      removed outlier: 3.738A  pdb=" N   PHE A  65 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 79
    Processing helix  chain 'A' and resid 81 through 89
    Processing helix  chain 'A' and resid 90 through 93
      removed outlier: 3.652A  pdb=" N   ALA A  93 " --> pdb=" O   GLY A  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 90 through 93'
    Processing helix  chain 'A' and resid 94 through 104
    Processing helix  chain 'A' and resid 106 through 120
      removed outlier: 4.085A  pdb=" N   GLU A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU A 114 " --> pdb=" O   PHE A 110 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 115 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLN A 118 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 134 through 165
      removed outlier: 3.644A  pdb=" N   GLY A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ASN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER A 165 " --> pdb=" O   TYR A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 234 through 253
      removed outlier: 3.863A  pdb=" N   CYS A 240 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 267
      removed outlier: 3.838A  pdb=" N   SER A 259 " --> pdb=" O   GLY A 255 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS A 261 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ILE A 265 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 282
      removed outlier: 3.611A  pdb=" N   PHE A 272 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.889A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 320
      removed outlier: 3.505A  pdb=" N   THR A 313 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 330
    Processing helix  chain 'A' and resid 338 through 372
      removed outlier: 3.699A  pdb=" N   ASP A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A 359 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA A 360 " --> pdb=" O   VAL A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 3.585A  pdb=" N   VAL A 387 " --> pdb=" O   GLY A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 397
      removed outlier: 3.863A  pdb=" N   THR A 397 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.632A  pdb=" N   TRP A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE A 409 " --> pdb=" O   ALA A 405 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASP A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER A 419 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 427 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASP A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 441
      removed outlier: 4.151A  pdb=" N   ARG A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   HIS A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 436 through 441'
    Processing helix  chain 'A' and resid 441 through 457
      removed outlier: 3.772A  pdb=" N   PHE A 447 " --> pdb=" O   LYS A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 494
      removed outlier: 4.435A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 510
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.918A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TRP A 556 " --> pdb=" O   PRO A 552 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET A 566 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 580
    Processing helix  chain 'A' and resid 583 through 589
    Processing helix  chain 'A' and resid 597 through 603
      removed outlier: 3.917A  pdb=" N   VAL A 601 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
      removed outlier: 3.792A  pdb=" N   PHE A 609 " --> pdb=" O   ILE A 606 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 606 through 609'
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 4.031A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 61 through 74
      removed outlier: 3.792A  pdb=" N   PHE E  65 " --> pdb=" O   LYS E  61 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU E  66 " --> pdb=" O   LYS E  62 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL E  70 " --> pdb=" O   LEU E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 95 through 105
    Processing helix  chain 'E' and resid 105 through 121
    Processing helix  chain 'E' and resid 131 through 134
    Processing helix  chain 'E' and resid 135 through 166
      removed outlier: 4.071A  pdb=" N   TYR E 139 " --> pdb=" O   LYS E 135 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR E 151 " --> pdb=" O   TYR E 147 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   VAL E 154 " --> pdb=" O   PHE E 150 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 215
    Processing helix  chain 'E' and resid 234 through 253
    Processing helix  chain 'E' and resid 255 through 267
    Processing helix  chain 'E' and resid 269 through 284
      removed outlier: 4.462A  pdb=" N   VAL E 273 " --> pdb=" O   LEU E 269 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LEU E 274 " --> pdb=" O   PRO E 270 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   THR E 283 " --> pdb=" O   VAL E 279 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU E 284 " --> pdb=" O   HIS E 280 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 287 through 295
      removed outlier: 4.048A  pdb=" N   ILE E 291 " --> pdb=" O   ALA E 287 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 308 through 320
      removed outlier: 3.639A  pdb=" N   ALA E 312 " --> pdb=" O   TRP E 308 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 324 through 333
      removed outlier: 3.745A  pdb=" N   TYR E 332 " --> pdb=" O   ALA E 328 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 338 through 372
    Processing helix  chain 'E' and resid 385 through 398
      Proline residue:  E 392  - end of helix
    Processing helix  chain 'E' and resid 400 through 435
    Processing helix  chain 'E' and resid 435 through 441
    Processing helix  chain 'E' and resid 441 through 457
    Processing helix  chain 'E' and resid 464 through 494
      removed outlier: 3.958A  pdb=" N   VAL E 468 " --> pdb=" O   GLY E 464 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 497 through 509
    Processing helix  chain 'E' and resid 514 through 523
    Processing helix  chain 'E' and resid 523 through 539
    Processing helix  chain 'E' and resid 551 through 567
      removed outlier: 4.024A  pdb=" N   ASN E 555 " --> pdb=" O   PRO E 551 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TRP E 556 " --> pdb=" O   PRO E 552 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER E 565 " --> pdb=" O   ILE E 561 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 567 through 580
    Processing helix  chain 'E' and resid 583 through 593
    Processing helix  chain 'E' and resid 598 through 603
      removed outlier: 3.933A  pdb=" N   ALA E 602 " --> pdb=" O   HIS E 598 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 610 through 616
      removed outlier: 4.066A  pdb=" N   TRP E 614 " --> pdb=" O   GLN E 610 " (cutoff:3.500A)

    527 hydrogen bonds defined for protein.
    1572 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.75

  Time building geometry restraints manager: 3.06 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 122
        2.68 -     3.24: 9022
        3.24 -     3.79: 14631
        3.79 -     4.35: 19640
        4.35 -     4.90: 32766
  Nonbonded interactions: 76181
  Sorted by model distance:
  nonbonded pdb=" C20 TP0 A 701 "
            pdb=" C29 TP0 A 701 "
     model   vdw
     2.127 3.088
  nonbonded pdb=" OG  SER A 318 "
            pdb="CL    CL A 703 "
     model   vdw
     2.227 3.190
  nonbonded pdb=" N   LYS E 129 "
            pdb=" N   ILE E 130 "
     model   vdw
     2.244 2.560
  nonbonded pdb=" O   SER A 251 "
            pdb=" OG1 THR A 258 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR E 332 "
            pdb=" OG1 THR E 429 "
     model   vdw
     2.295 3.040
  ... (remaining 76176 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 53 through 617)
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     23.950
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.300
-------------------------------------------------------------------------------
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= 0.194
  Angle     :  0.603  17.108  12757  Z= 0.367
  Chirality :  0.035   0.224   1418
  Planarity :  0.004   0.048   1554
  Dihedral  : 11.793 143.867   3145
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  :  7.14 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.23), residues: 1126
  helix: -0.76 (0.18), residues: 730
  sheet:  None (None), residues: 0
  loop : -1.94 (0.29), residues: 396

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

*********************** 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  : 1.026 
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: 0.8430
  time to fit residues: 258.1946
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  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain E residue  131 CYS
Chi-restraints excluded: chain E residue  133 PHE
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  180 TRP
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  205 TYR
Chi-restraints excluded: chain E residue  359 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 33 optimal weight:    0.2980
   chunk 53 optimal weight:    0.2980
   chunk 65 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 153 ASN
A 184 ASN
A 280 HIS
A 350 ASN
A 507 GLN
E 120 ASN
E 153 ASN
E 337 ASN
E 613 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.182388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.151455 restraints weight = 12317.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 2.10
r_work: 0.3783 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2943

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= 0.185
  Angle     :  0.580  10.658  12757  Z= 0.289
  Chirality :  0.039   0.170   1418
  Planarity :  0.004   0.030   1554
  Dihedral  :  8.044 140.919   1242
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 17.65 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.25), residues: 1126
  helix:  0.43 (0.19), residues: 753
  sheet:  None (None), residues: 0
  loop : -1.46 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 128 
 HIS   0.006   0.001   HIS E 613 
 PHE   0.020   0.001   PHE E 275 
 TYR   0.016   0.001   TYR A 111 
 ARG   0.005   0.001   ARG A 604 

*********************** 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
  205 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 162
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: A  297 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7961 (pt)
REVERT: A  439 LYS cc_start: 0.8813 (mttt) cc_final: 0.8442 (mtpm)
REVERT: A  585 TRP cc_start: 0.7142 (m100) cc_final: 0.6614 (m-10)
REVERT: A  595 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7491 (mp0)
REVERT: E  100 LEU cc_start: 0.8311 (tt) cc_final: 0.7228 (mm)
REVERT: E  119 TYR cc_start: 0.6890 (t80) cc_final: 0.6513 (t80)
REVERT: E  120 ASN cc_start: 0.8313 (m110) cc_final: 0.8056 (m-40)
REVERT: E  121 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7859 (mpt90)
REVERT: E  242 MET cc_start: 0.7633 (mtm) cc_final: 0.7374 (mtt)
REVERT: E  436 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8236 (mp10)
REVERT: E  438 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8109 (mm)
REVERT: E  603 GLN cc_start: 0.6947 (mt0) cc_final: 0.6689 (mp10)
  outliers start: 43
  outliers final: 15
  residues processed: 188
  average time/residue: 0.8154
  time to fit residues: 169.3883
Evaluate side-chains
  147 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
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  297 ILE
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  137 VAL
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain E residue  180 TRP
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  436 GLN
Chi-restraints excluded: chain E residue  438 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.8982

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.180510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.146893 restraints weight = 12531.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 2.31
r_work: 0.3774 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9349  Z= 0.191
  Angle     :  0.571  15.409  12757  Z= 0.280
  Chirality :  0.039   0.143   1418
  Planarity :  0.004   0.029   1554
  Dihedral  :  7.765 141.673   1235
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.38 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.25), residues: 1126
  helix:  0.96 (0.19), residues: 740
  sheet:  None (None), residues: 0
  loop : -1.05 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 128 
 HIS   0.008   0.001   HIS E 370 
 PHE   0.019   0.001   PHE A 362 
 TYR   0.017   0.001   TYR E 340 
 ARG   0.009   0.001   ARG A 512 

*********************** 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
  187 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 142
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8121 (pptt) cc_final: 0.7884 (pptt)
REVERT: A  391 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7459 (m-80)
REVERT: A  439 LYS cc_start: 0.8662 (mttt) cc_final: 0.8359 (mtpm)
REVERT: A  585 TRP cc_start: 0.7075 (m100) cc_final: 0.6672 (m-10)
REVERT: A  595 GLU cc_start: 0.7582 (mp0) cc_final: 0.7378 (mp0)
REVERT: E  100 LEU cc_start: 0.8410 (tt) cc_final: 0.7357 (mm)
REVERT: E  111 TYR cc_start: 0.8659 (t80) cc_final: 0.8457 (t80)
REVERT: E  112 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7928 (ttt)
REVERT: E  119 TYR cc_start: 0.6848 (t80) cc_final: 0.6406 (t80)
REVERT: E  121 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7753 (mmm160)
REVERT: E  242 MET cc_start: 0.7425 (mtm) cc_final: 0.7149 (mtt)
REVERT: E  337 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6483 (p0)
REVERT: E  340 TYR cc_start: 0.6933 (t80) cc_final: 0.6704 (t80)
REVERT: E  438 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8204 (mm)
REVERT: E  479 THR cc_start: 0.6676 (m) cc_final: 0.6015 (t)
REVERT: E  508 MET cc_start: 0.5767 (ttm) cc_final: 0.5508 (ttm)
REVERT: E  600 LEU cc_start: 0.7399 (mm) cc_final: 0.6970 (mp)
REVERT: E  603 GLN cc_start: 0.6862 (mt0) cc_final: 0.6642 (mp10)
  outliers start: 45
  outliers final: 17
  residues processed: 172
  average time/residue: 0.7438
  time to fit residues: 142.7348
Evaluate side-chains
  146 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  565 SER
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  112 MET
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  180 TRP
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  296 HIS
Chi-restraints excluded: chain E residue  337 ASN
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  486 LEU
Chi-restraints excluded: chain E residue  566 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 81 optimal weight:    9.9990
   chunk 57 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 90 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.7384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.165398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.132405 restraints weight = 12470.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 1.97
r_work: 0.3525 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9349  Z= 0.284
  Angle     :  0.627  15.354  12757  Z= 0.313
  Chirality :  0.041   0.141   1418
  Planarity :  0.004   0.030   1554
  Dihedral  :  7.821 141.183   1233
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 18.28 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1126
  helix:  0.87 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop : -0.86 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  80 
 HIS   0.008   0.001   HIS E 370 
 PHE   0.024   0.002   PHE A 362 
 TYR   0.018   0.002   TYR A 340 
 ARG   0.008   0.001   ARG A 512 

*********************** 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
  176 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 127
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8086 (pptt) cc_final: 0.7782 (pptt)
REVERT: A  439 LYS cc_start: 0.8747 (mttt) cc_final: 0.8376 (mtpm)
REVERT: A  585 TRP cc_start: 0.7213 (m100) cc_final: 0.6679 (m-10)
REVERT: A  595 GLU cc_start: 0.7877 (mp0) cc_final: 0.7624 (mp0)
REVERT: A  597 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7808 (mt-10)
REVERT: E  100 LEU cc_start: 0.8600 (tt) cc_final: 0.7538 (mm)
REVERT: E  119 TYR cc_start: 0.7033 (t80) cc_final: 0.6508 (t80)
REVERT: E  121 ARG cc_start: 0.8106 (tpp80) cc_final: 0.7851 (mpt90)
REVERT: E  190 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6112 (tt)
REVERT: E  242 MET cc_start: 0.7575 (mtm) cc_final: 0.7292 (mtt)
REVERT: E  254 LYS cc_start: 0.7682 (tptm) cc_final: 0.7161 (tppt)
REVERT: E  257 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5369 (mmmt)
REVERT: E  337 ASN cc_start: 0.7029 (OUTLIER) cc_final: 0.6445 (p0)
REVERT: E  438 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8152 (mm)
REVERT: E  461 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7886 (pp)
REVERT: E  566 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7658 (mtm)
  outliers start: 49
  outliers final: 19
  residues processed: 163
  average time/residue: 0.8300
  time to fit residues: 149.8846
Evaluate side-chains
  140 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  481 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  190 LEU
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  337 ASN
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  534 VAL
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:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   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 = 0.4084 r_free = 0.4084 target = 0.168793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.136042 restraints weight = 12393.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 1.94
r_work: 0.3565 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.4401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9349  Z= 0.177
  Angle     :  0.583  16.430  12757  Z= 0.281
  Chirality :  0.038   0.128   1418
  Planarity :  0.003   0.028   1554
  Dihedral  :  7.584 140.784   1230
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 19.96 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1126
  helix:  1.19 (0.20), residues: 739
  sheet:  None (None), residues: 0
  loop : -0.77 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  80 
 HIS   0.004   0.001   HIS E 598 
 PHE   0.019   0.001   PHE A 362 
 TYR   0.012   0.001   TYR A 340 
 ARG   0.004   0.000   ARG A 512 

*********************** 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
  168 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 123
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8024 (pptt) cc_final: 0.7648 (pptt)
REVERT: A  425 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8279 (tp30)
REVERT: A  439 LYS cc_start: 0.8754 (mttt) cc_final: 0.8381 (mtpm)
REVERT: A  581 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7882 (tm-30)
REVERT: A  585 TRP cc_start: 0.7164 (m100) cc_final: 0.6685 (m-10)
REVERT: A  595 GLU cc_start: 0.7774 (mp0) cc_final: 0.7540 (mp0)
REVERT: E  100 LEU cc_start: 0.8519 (tt) cc_final: 0.7435 (mm)
REVERT: E  112 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8020 (ttp)
REVERT: E  119 TYR cc_start: 0.7023 (t80) cc_final: 0.6501 (t80)
REVERT: E  121 ARG cc_start: 0.8073 (tpp80) cc_final: 0.7862 (mpt90)
REVERT: E  242 MET cc_start: 0.7520 (mtm) cc_final: 0.7228 (mtt)
REVERT: E  254 LYS cc_start: 0.7654 (tptm) cc_final: 0.7113 (tppt)
REVERT: E  257 LYS cc_start: 0.5903 (OUTLIER) cc_final: 0.5359 (mmmt)
REVERT: E  438 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8116 (mm)
REVERT: E  461 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7978 (pp)
REVERT: E  600 LEU cc_start: 0.7137 (mm) cc_final: 0.6834 (mp)
  outliers start: 45
  outliers final: 18
  residues processed: 155
  average time/residue: 0.7756
  time to fit residues: 133.6365
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  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  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  112 MET
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  180 TRP
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 101 optimal weight:    0.1980
   chunk 12 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 60 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 14 optimal weight:   20.0000
   chunk 94 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0670
   overall best weight:    0.9322

-------------------------------------------------------------------------------
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 = 0.4245 r_free = 0.4245 target = 0.176416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.139830 restraints weight = 12283.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3839 rms_B_bonded: 2.28
r_work: 0.3721 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3587 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.4567

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= 0.192
  Angle     :  0.591  17.193  12757  Z= 0.286
  Chirality :  0.039   0.196   1418
  Planarity :  0.004   0.054   1554
  Dihedral  :  7.589 140.617   1229
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.48 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.26), residues: 1126
  helix:  1.22 (0.19), residues: 745
  sheet:  None (None), residues: 0
  loop : -0.75 (0.34), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E  80 
 HIS   0.006   0.001   HIS E 370 
 PHE   0.020   0.001   PHE A 362 
 TYR   0.018   0.001   TYR E 340 
 ARG   0.004   0.000   ARG A 512 

*********************** 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
  159 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 115
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.8023 (pptt) cc_final: 0.7588 (pptt)
REVERT: A  439 LYS cc_start: 0.8762 (mttt) cc_final: 0.8388 (mtpm)
REVERT: A  581 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7947 (tm-30)
REVERT: A  585 TRP cc_start: 0.7191 (m100) cc_final: 0.6674 (m-10)
REVERT: A  595 GLU cc_start: 0.7924 (mp0) cc_final: 0.7648 (mp0)
REVERT: E  100 LEU cc_start: 0.8565 (tt) cc_final: 0.7434 (mm)
REVERT: E  112 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8062 (ttp)
REVERT: E  119 TYR cc_start: 0.7006 (t80) cc_final: 0.6583 (t80)
REVERT: E  121 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7739 (mpt90)
REVERT: E  242 MET cc_start: 0.7606 (mtm) cc_final: 0.7294 (mtt)
REVERT: E  254 LYS cc_start: 0.7654 (tptm) cc_final: 0.7082 (tppt)
REVERT: E  257 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5281 (mtpm)
REVERT: E  370 HIS cc_start: 0.4857 (OUTLIER) cc_final: 0.4657 (p90)
REVERT: E  377 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6432 (mt-10)
REVERT: E  438 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8126 (mm)
REVERT: E  461 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7958 (pp)
REVERT: E  479 THR cc_start: 0.6918 (m) cc_final: 0.6207 (t)
REVERT: E  600 LEU cc_start: 0.7159 (mm) cc_final: 0.6859 (mp)
  outliers start: 44
  outliers final: 21
  residues processed: 147
  average time/residue: 0.7901
  time to fit residues: 128.9514
Evaluate side-chains
  135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  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  596 ASN
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  112 MET
Chi-restraints excluded: chain E residue  137 VAL
Chi-restraints excluded: chain E residue  180 TRP
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  370 HIS
Chi-restraints excluded: chain E residue  377 GLU
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  390 LEU
Chi-restraints excluded: chain E residue  438 LEU
Chi-restraints excluded: chain E residue  461 ILE
Chi-restraints excluded: chain E residue  603 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 98 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 106 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 110 optimal weight:    7.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.176865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.142606 restraints weight = 12289.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 2.18
r_work: 0.3753 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3615 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.4603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9349  Z= 0.166
  Angle     :  0.590  17.019  12757  Z= 0.283
  Chirality :  0.039   0.177   1418
  Planarity :  0.003   0.040   1554
  Dihedral  :  7.561 140.454   1229
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.22 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1126
  helix:  1.34 (0.19), residues: 745
  sheet:  None (None), residues: 0
  loop : -0.76 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP E  80 
 HIS   0.005   0.001   HIS E 370 
 PHE   0.019   0.001   PHE A 362 
 TYR   0.011   0.001   TYR A 340 
 ARG   0.003   0.000   ARG A 512 

*********************** 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
  156 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 116
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7855 (pptt) cc_final: 0.7409 (pptt)
REVERT: A  425 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8316 (tp30)
REVERT: A  439 LYS cc_start: 0.8726 (mttt) cc_final: 0.8366 (mtpm)
REVERT: A  581 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7948 (tm-30)
REVERT: A  585 TRP cc_start: 0.7165 (m100) cc_final: 0.6667 (m-10)
REVERT: A  595 GLU cc_start: 0.7828 (mp0) cc_final: 0.7538 (mp0)
REVERT: E  112 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8023 (ttp)
REVERT: E  119 TYR cc_start: 0.6971 (t80) cc_final: 0.6503 (t80)
REVERT: E  121 ARG cc_start: 0.8016 (tpp80) cc_final: 0.7666 (mpt90)
REVERT: E  242 MET cc_start: 0.7611 (mtm) cc_final: 0.7309 (mtt)
REVERT: E  254 LYS cc_start: 0.7634 (tptm) cc_final: 0.7074 (tppt)
REVERT: E  257 LYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5280 (mtpm)
REVERT: E  370 HIS cc_start: 0.4721 (OUTLIER) cc_final: 0.4519 (p90)
REVERT: E  377 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6404 (mt-10)
REVERT: E  438 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8090 (mm)
REVERT: E  461 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7939 (pp)
REVERT: E  479 THR cc_start: 0.6739 (m) cc_final: 0.6083 (t)
REVERT: E  584 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4592 (tt)
REVERT: E  600 LEU cc_start: 0.7185 (mm) cc_final: 0.6878 (mp)
  outliers start: 40
  outliers final: 18
  residues processed: 147
  average time/residue: 0.8160
  time to fit residues: 132.7547
Evaluate side-chains
  137 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  236 GLN
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  112 MET
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  370 HIS
Chi-restraints excluded: chain E residue  377 GLU
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  603 GLN
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 1 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4223 r_free = 0.4223 target = 0.173363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.137990 restraints weight = 12440.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.24
r_work: 0.3688 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.4817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9349  Z= 0.237
  Angle     :  0.645  18.190  12757  Z= 0.308
  Chirality :  0.040   0.189   1418
  Planarity :  0.004   0.047   1554
  Dihedral  :  7.655 140.465   1229
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 21.22 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1126
  helix:  1.26 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.66 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E  80 
 HIS   0.005   0.001   HIS E 598 
 PHE   0.024   0.002   PHE E 275 
 TYR   0.017   0.001   TYR E 340 
 ARG   0.004   0.000   ARG A 512 

*********************** 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
  154 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 111
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7871 (pptt) cc_final: 0.7392 (pptt)
REVERT: A  439 LYS cc_start: 0.8771 (mttt) cc_final: 0.8403 (mtpm)
REVERT: A  581 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7973 (tm-30)
REVERT: A  585 TRP cc_start: 0.7221 (m100) cc_final: 0.6704 (m-10)
REVERT: E  112 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8084 (ttp)
REVERT: E  119 TYR cc_start: 0.6965 (t80) cc_final: 0.6507 (t80)
REVERT: E  121 ARG cc_start: 0.8043 (tpp80) cc_final: 0.7653 (mpt90)
REVERT: E  242 MET cc_start: 0.7683 (mtm) cc_final: 0.7365 (mtt)
REVERT: E  254 LYS cc_start: 0.7641 (tptm) cc_final: 0.7087 (tppt)
REVERT: E  257 LYS cc_start: 0.6016 (OUTLIER) cc_final: 0.5324 (mtpm)
REVERT: E  370 HIS cc_start: 0.4757 (OUTLIER) cc_final: 0.4338 (p90)
REVERT: E  377 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6409 (mt-10)
REVERT: E  438 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8113 (mm)
REVERT: E  461 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7888 (pp)
REVERT: E  479 THR cc_start: 0.6816 (m) cc_final: 0.6269 (t)
REVERT: E  584 LEU cc_start: 0.4969 (OUTLIER) cc_final: 0.4597 (tt)
REVERT: E  598 HIS cc_start: 0.5924 (OUTLIER) cc_final: 0.4957 (m-70)
REVERT: E  600 LEU cc_start: 0.7151 (mm) cc_final: 0.6836 (mp)
REVERT: E  612 GLN cc_start: 0.6855 (tm-30) cc_final: 0.6535 (tp40)
  outliers start: 43
  outliers final: 21
  residues processed: 145
  average time/residue: 0.8303
  time to fit residues: 133.0750
Evaluate side-chains
  136 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  313 THR
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  137 VAL
Chi-restraints excluded: chain E residue  171 LEU
Chi-restraints excluded: chain E residue  199 HIS
Chi-restraints excluded: chain E residue  257 LYS
Chi-restraints excluded: chain E residue  278 LEU
Chi-restraints excluded: chain E residue  359 PHE
Chi-restraints excluded: chain E residue  370 HIS
Chi-restraints excluded: chain E residue  377 GLU
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
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  598 HIS
Chi-restraints excluded: chain E residue  603 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 56 optimal weight:   20.0000
   chunk 81 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 599 HIS
** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4228 r_free = 0.4228 target = 0.173971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.139064 restraints weight = 12158.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 2.18
r_work: 0.3713 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3582 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9349  Z= 0.209
  Angle     :  0.639  18.704  12757  Z= 0.304
  Chirality :  0.040   0.175   1418
  Planarity :  0.004   0.041   1554
  Dihedral  :  7.638 140.384   1229
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.95 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1126
  helix:  1.29 (0.19), residues: 745
  sheet:  None (None), residues: 0
  loop : -0.60 (0.34), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E  80 
 HIS   0.007   0.001   HIS E 370 
 PHE   0.020   0.001   PHE A 362 
 TYR   0.013   0.001   TYR A 340 
 ARG   0.003   0.000   ARG A 512 

*********************** 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
  145 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7839 (pptt) cc_final: 0.7375 (pptt)
REVERT: A  439 LYS cc_start: 0.8774 (mttt) cc_final: 0.8404 (mtpm)
REVERT: A  585 TRP cc_start: 0.7195 (m100) cc_final: 0.6706 (m-10)
REVERT: E  112 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8098 (ttp)
REVERT: E  119 TYR cc_start: 0.6948 (t80) cc_final: 0.6526 (t80)
REVERT: E  121 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7649 (mpt90)
REVERT: E  242 MET cc_start: 0.7638 (mtm) cc_final: 0.7301 (mtt)
REVERT: E  254 LYS cc_start: 0.7629 (tptm) cc_final: 0.7082 (tppt)
REVERT: E  257 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5293 (mtpm)
REVERT: E  377 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6367 (mt-10)
REVERT: E  438 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8119 (mm)
REVERT: E  461 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7863 (pp)
REVERT: E  479 THR cc_start: 0.6631 (m) cc_final: 0.6162 (t)
REVERT: E  584 LEU cc_start: 0.5003 (OUTLIER) cc_final: 0.4652 (tt)
REVERT: E  598 HIS cc_start: 0.5829 (OUTLIER) cc_final: 0.4990 (m-70)
REVERT: E  600 LEU cc_start: 0.7159 (mm) cc_final: 0.6838 (mp)
  outliers start: 36
  outliers final: 21
  residues processed: 134
  average time/residue: 0.7943
  time to fit residues: 118.1167
Evaluate side-chains
  136 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  313 THR
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  611 LEU
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  112 MET
Chi-restraints excluded: chain E residue  133 PHE
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  377 GLU
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  411 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
Chi-restraints excluded: chain E residue  584 LEU
Chi-restraints excluded: chain E residue  598 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 111 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 109 optimal weight:    7.9990
   chunk 78 optimal weight:    9.9990
   chunk 59 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4208 r_free = 0.4208 target = 0.172078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.137167 restraints weight = 12408.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.19
r_work: 0.3689 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3557 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.4989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9349  Z= 0.252
  Angle     :  0.669  17.207  12757  Z= 0.319
  Chirality :  0.040   0.135   1418
  Planarity :  0.004   0.037   1554
  Dihedral  :  7.716 140.414   1229
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.16 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.26), residues: 1126
  helix:  1.15 (0.19), residues: 753
  sheet:  None (None), residues: 0
  loop : -0.45 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E  80 
 HIS   0.009   0.001   HIS E 370 
 PHE   0.035   0.002   PHE A 275 
 TYR   0.017   0.001   TYR E 340 
 ARG   0.004   0.000   ARG A 512 

********************** 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
  145 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 110
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 LYS cc_start: 0.7797 (pptt) cc_final: 0.7321 (pptt)
REVERT: A  304 GLU cc_start: 0.6658 (mp0) cc_final: 0.6445 (mp0)
REVERT: A  439 LYS cc_start: 0.8761 (mttt) cc_final: 0.8381 (mtpm)
REVERT: A  581 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8021 (tm-30)
REVERT: A  585 TRP cc_start: 0.7197 (m100) cc_final: 0.6720 (m-10)
REVERT: E  112 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8115 (ttp)
REVERT: E  119 TYR cc_start: 0.6950 (t80) cc_final: 0.6506 (t80)
REVERT: E  121 ARG cc_start: 0.8016 (tpp80) cc_final: 0.7597 (mpt90)
REVERT: E  242 MET cc_start: 0.7663 (mtm) cc_final: 0.7324 (mtt)
REVERT: E  254 LYS cc_start: 0.7671 (tptm) cc_final: 0.7151 (tppt)
REVERT: E  257 LYS cc_start: 0.5912 (OUTLIER) cc_final: 0.5210 (mtpm)
REVERT: E  377 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6419 (mt-10)
REVERT: E  438 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8132 (mm)
REVERT: E  461 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7814 (pp)
REVERT: E  479 THR cc_start: 0.6695 (m) cc_final: 0.6204 (t)
REVERT: E  584 LEU cc_start: 0.5015 (OUTLIER) cc_final: 0.4626 (tt)
REVERT: E  598 HIS cc_start: 0.5797 (OUTLIER) cc_final: 0.5000 (m-70)
REVERT: E  600 LEU cc_start: 0.7096 (mm) cc_final: 0.6784 (mp)
  outliers start: 35
  outliers final: 20
  residues processed: 138
  average time/residue: 0.8238
  time to fit residues: 126.0686
Evaluate side-chains
  135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  200 THR
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  313 THR
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  581 GLN
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  612 GLN
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain E residue  112 MET
Chi-restraints excluded: chain E residue  133 PHE
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  377 GLU
Chi-restraints excluded: chain E residue  381 THR
Chi-restraints excluded: chain E residue  411 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0670
   chunk 101 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
** E 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4238 r_free = 0.4238 target = 0.175004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.140695 restraints weight = 12291.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3847 rms_B_bonded: 2.16
r_work: 0.3731 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.4919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9349  Z= 0.179
  Angle     :  0.621  16.765  12757  Z= 0.296
  Chirality :  0.040   0.470   1418
  Planarity :  0.003   0.035   1554
  Dihedral  :  7.588 140.368   1229
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 22.27 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1126
  helix:  1.28 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop : -0.47 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E  80 
 HIS   0.006   0.001   HIS E 370 
 PHE   0.019   0.001   PHE A 362 
 TYR   0.012   0.001   TYR A 340 
 ARG   0.003   0.000   ARG A 512 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6411.62 seconds
wall clock time: 114 minutes 7.82 seconds (6847.82 seconds total)