Starting phenix.real_space_refine
on Mon Apr  6 07:06:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dby_27317/04_2026/8dby_27317.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dby_27317/04_2026/8dby_27317.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dby_27317/04_2026/8dby_27317.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dby_27317/04_2026/8dby_27317.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dby_27317/04_2026/8dby_27317.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dby_27317/04_2026/8dby_27317.map"
  }
  resolution = 2.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.033
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
     Mo      2     10.26       5
     Fe     32      7.16       5
     S     138      5.16       5
     C   10168      2.51       5
     N    2702      2.21       5
     O    3752      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16794
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 3790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 477, 3790
          Classifications: {'peptide': 477}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455}
    Chain: "B"
      Number of atoms: 4174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 522, 4174
          Classifications: {'peptide': 522}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495}
    Chain: "C"
      Number of atoms: 3790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 477, 3790
          Classifications: {'peptide': 477}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455}
    Chain: "D"
      Number of atoms: 4174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 522, 4174
          Classifications: {'peptide': 522}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {'HCA': 1, 'ICS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 3, 17
          Unusual residues: {' FE': 2, 'CLF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {'HCA': 1, 'ICS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 1, 15
          Unusual residues: {'CLF': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 129
          Classifications: {'water': 129}
          Link IDs: {None: 128}
    Chain: "B"
      Number of atoms: 249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 249
          Classifications: {'water': 249}
          Link IDs: {None: 248}
    Chain: "C"
      Number of atoms: 136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 136
          Classifications: {'water': 136}
          Link IDs: {None: 135}
    Chain: "D"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 256
          Classifications: {'water': 256}
          Link IDs: {None: 255}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2089  SG  CYS A 275      24.390  52.573  58.418  1.00 35.40           S
  ATOM   1170  SG  CYS A 154      22.651  33.615  46.326  1.00 25.15           S
  ATOM   4549  SG  CYS B  95      26.918  35.091  43.479  1.00 38.94           S
  ATOM    465  SG  CYS A  62      25.806  38.893  48.750  1.00 22.00           S
  ATOM    652  SG  CYS A  88      28.585  32.914  48.465  1.00 33.57           S
  ATOM    652  SG  CYS A  88      28.585  32.914  48.465  1.00 33.57           S
  ATOM   5002  SG  CYS B 153      25.800  30.059  44.880  1.00 36.56           S
  ATOM   4369  SG  CYS B  70      32.605  31.514  43.370  1.00 32.38           S
  ATOM   4549  SG  CYS B  95      26.918  35.091  43.479  1.00 38.94           S
  ATOM  10053  SG  CYS C 275      99.106  31.918  58.411  1.00 35.78           S
  ATOM   9134  SG  CYS C 154     100.854  50.890  46.325  1.00 25.77           S
  ATOM  12513  SG  CYS D  95      96.494  49.486  43.498  1.00 38.34           S
  ATOM   8429  SG  CYS C  62      97.708  45.674  48.642  1.00 21.26           S
  ATOM   8616  SG  CYS C  88      94.900  51.619  48.455  1.00 33.41           S
  ATOM   8616  SG  CYS C  88      94.900  51.619  48.455  1.00 33.41           S
  ATOM  12966  SG  CYS D 153      97.672  54.524  44.872  1.00 32.04           S
  ATOM  12333  SG  CYS D  70      90.851  52.973  43.337  1.00 33.74           S
  ATOM  12513  SG  CYS D  95      96.494  49.486  43.498  1.00 38.34           S

  Time building chain proxies: 3.88, per 1000 atoms: 0.23
  Number of scatterers: 16794
  At special positions: 0
  Unit cell: (124.15, 85.15, 94.9, 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)
     Mo      2     41.97
     Fe     32     26.01
     S     138     16.00
     O    3752      8.00
     N    2702      7.00
     C   10168      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=17, symmetry=0
  Number of additional bonds: simple=17, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.47
  Conformation dependent library (CDL) restraints added in 760.7 milliseconds
  

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3664

  Finding SS restraints...
    Secondary structure from input PDB file:
      106 helices and 12 sheets defined
      58.8% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 18
    Processing helix  chain 'A' and resid 21 through 30
      removed outlier: 4.036A  pdb=" N   LYS A  30 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 3.707A  pdb=" N   LYS A  44 " --> pdb=" O   GLN A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 68
    Processing helix  chain 'A' and resid 86 through 92
    Processing helix  chain 'A' and resid 119 through 126
    Processing helix  chain 'A' and resid 127 through 142
    Processing helix  chain 'A' and resid 154 through 158
    Processing helix  chain 'A' and resid 162 through 175
      removed outlier: 3.666A  pdb=" N   VAL A 166 " --> pdb=" O   ASP A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 206
      removed outlier: 4.166A  pdb=" N   GLY A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 210
      removed outlier: 4.685A  pdb=" N   ARG A 210 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 207 through 210'
    Processing helix  chain 'A' and resid 233 through 245
      removed outlier: 3.862A  pdb=" N   LEU A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 265
    Processing helix  chain 'A' and resid 266 through 268
      No H-bonds generated for 'chain 'A' and resid 266 through 268'
    Processing helix  chain 'A' and resid 275 through 291
      removed outlier: 5.714A  pdb=" N   TYR A 281 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   ILE A 282 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 314
    Processing helix  chain 'A' and resid 317 through 347
      Proline residue:  A 333  - end of helix
      Proline residue:  A 344  - end of helix
    Processing helix  chain 'A' and resid 358 through 363
    Processing helix  chain 'A' and resid 363 through 369
    Processing helix  chain 'A' and resid 383 through 394
      removed outlier: 4.296A  pdb=" N   LYS A 392 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLU A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 417
    Processing helix  chain 'A' and resid 424 through 434
      removed outlier: 4.480A  pdb=" N   PHE A 429 " --> pdb=" O   ILE A 425 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   ILE A 430 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 447
    Processing helix  chain 'A' and resid 451 through 468
    Processing helix  chain 'A' and resid 469 through 474
    Processing helix  chain 'B' and resid 10 through 15
    Processing helix  chain 'B' and resid 17 through 31
    Processing helix  chain 'B' and resid 36 through 48
    Processing helix  chain 'B' and resid 49 through 58
    Processing helix  chain 'B' and resid 70 through 81
      removed outlier: 4.023A  pdb=" N   GLY B  74 " --> pdb=" O   CYS B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 108
      removed outlier: 3.937A  pdb=" N   VAL B  96 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 3.983A  pdb=" N   PHE B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 143
    Processing helix  chain 'B' and resid 152 through 159
    Processing helix  chain 'B' and resid 161 through 172
    Processing helix  chain 'B' and resid 192 through 210
    Processing helix  chain 'B' and resid 211 through 213
      No H-bonds generated for 'chain 'B' and resid 211 through 213'
    Processing helix  chain 'B' and resid 233 through 247
      removed outlier: 3.800A  pdb=" N   PHE B 237 " --> pdb=" O   TYR B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 284
    Processing helix  chain 'B' and resid 285 through 287
      No H-bonds generated for 'chain 'B' and resid 285 through 287'
    Processing helix  chain 'B' and resid 294 through 297
    Processing helix  chain 'B' and resid 298 through 308
    Processing helix  chain 'B' and resid 322 through 337
    Processing helix  chain 'B' and resid 341 through 363
      removed outlier: 5.199A  pdb=" N   THR B 360 " --> pdb=" O   THR B 356 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   TRP B 361 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 386
    Processing helix  chain 'B' and resid 399 through 412
    Processing helix  chain 'B' and resid 413 through 417
      removed outlier: 3.630A  pdb=" N   LYS B 417 " --> pdb=" O   PRO B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 437
    Processing helix  chain 'B' and resid 447 through 459
      removed outlier: 4.375A  pdb=" N   ILE B 451 " --> pdb=" O   TYR B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 463
    Processing helix  chain 'B' and resid 478 through 482
    Processing helix  chain 'B' and resid 485 through 509
    Processing helix  chain 'B' and resid 515 through 519
    Processing helix  chain 'C' and resid 5 through 18
    Processing helix  chain 'C' and resid 21 through 30
      removed outlier: 4.025A  pdb=" N   LYS C  30 " --> pdb=" O   LYS C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 45
      removed outlier: 3.711A  pdb=" N   LYS C  44 " --> pdb=" O   GLN C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 68
    Processing helix  chain 'C' and resid 86 through 92
    Processing helix  chain 'C' and resid 119 through 126
    Processing helix  chain 'C' and resid 127 through 142
    Processing helix  chain 'C' and resid 154 through 158
    Processing helix  chain 'C' and resid 162 through 175
      removed outlier: 3.670A  pdb=" N   VAL C 166 " --> pdb=" O   ASP C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 206
      removed outlier: 4.163A  pdb=" N   GLY C 194 " --> pdb=" O   SER C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 210
      removed outlier: 4.573A  pdb=" N   ARG C 210 " --> pdb=" O   LEU C 207 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 207 through 210'
    Processing helix  chain 'C' and resid 233 through 245
      removed outlier: 3.853A  pdb=" N   LEU C 241 " --> pdb=" O   SER C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 265
    Processing helix  chain 'C' and resid 266 through 268
      No H-bonds generated for 'chain 'C' and resid 266 through 268'
    Processing helix  chain 'C' and resid 275 through 291
      removed outlier: 5.698A  pdb=" N   TYR C 281 " --> pdb=" O   ARG C 277 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   ILE C 282 " --> pdb=" O   SER C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 314
    Processing helix  chain 'C' and resid 317 through 347
      Proline residue:  C 333  - end of helix
      Proline residue:  C 344  - end of helix
    Processing helix  chain 'C' and resid 358 through 363
    Processing helix  chain 'C' and resid 363 through 369
    Processing helix  chain 'C' and resid 383 through 394
      removed outlier: 4.309A  pdb=" N   LYS C 392 " --> pdb=" O   ASP C 388 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   GLU C 393 " --> pdb=" O   ARG C 389 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 417
    Processing helix  chain 'C' and resid 424 through 434
      removed outlier: 4.463A  pdb=" N   PHE C 429 " --> pdb=" O   ILE C 425 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   ILE C 430 " --> pdb=" O   LYS C 426 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 447
    Processing helix  chain 'C' and resid 451 through 468
    Processing helix  chain 'C' and resid 469 through 474
    Processing helix  chain 'D' and resid 10 through 15
    Processing helix  chain 'D' and resid 17 through 31
    Processing helix  chain 'D' and resid 36 through 48
    Processing helix  chain 'D' and resid 49 through 58
    Processing helix  chain 'D' and resid 70 through 81
      removed outlier: 4.023A  pdb=" N   GLY D  74 " --> pdb=" O   CYS D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 108
      removed outlier: 3.942A  pdb=" N   VAL D  96 " --> pdb=" O   SER D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 126
      removed outlier: 3.958A  pdb=" N   PHE D 125 " --> pdb=" O   ASP D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 143
    Processing helix  chain 'D' and resid 152 through 159
    Processing helix  chain 'D' and resid 161 through 172
    Processing helix  chain 'D' and resid 192 through 210
    Processing helix  chain 'D' and resid 211 through 213
      No H-bonds generated for 'chain 'D' and resid 211 through 213'
    Processing helix  chain 'D' and resid 233 through 247
      removed outlier: 3.823A  pdb=" N   PHE D 237 " --> pdb=" O   TYR D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 277 through 284
    Processing helix  chain 'D' and resid 285 through 287
      No H-bonds generated for 'chain 'D' and resid 285 through 287'
    Processing helix  chain 'D' and resid 294 through 297
    Processing helix  chain 'D' and resid 298 through 308
    Processing helix  chain 'D' and resid 322 through 337
    Processing helix  chain 'D' and resid 341 through 363
      removed outlier: 5.201A  pdb=" N   THR D 360 " --> pdb=" O   THR D 356 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   TRP D 361 " --> pdb=" O   ASP D 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 372 through 386
    Processing helix  chain 'D' and resid 399 through 412
    Processing helix  chain 'D' and resid 413 through 417
      removed outlier: 3.633A  pdb=" N   LYS D 417 " --> pdb=" O   PRO D 414 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 426 through 437
    Processing helix  chain 'D' and resid 447 through 459
      removed outlier: 4.376A  pdb=" N   ILE D 451 " --> pdb=" O   TYR D 447 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 460 through 463
    Processing helix  chain 'D' and resid 478 through 482
    Processing helix  chain 'D' and resid 485 through 509
    Processing helix  chain 'D' and resid 515 through 519
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34
      removed outlier: 6.128A  pdb=" N   VAL A 351 " --> pdb=" O   VAL A 374 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLY A 376 " --> pdb=" O   VAL A 351 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ARG A 350 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   GLY A 422 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   MET A 352 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   ILE A 421 " --> pdb=" O   ARG A 439 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181
      removed outlier: 4.141A  pdb=" N   PHE A 114 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254
      removed outlier: 7.195A  pdb=" N   ILE A 225 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   GLN A 252 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   GLY A 227 " --> pdb=" O   GLN A 252 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   SER A 254 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ASP A 222 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   LEU A 272 " --> pdb=" O   ASP A 222 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ALA A 224 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ASN A 271 " --> pdb=" O   MET A 295 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115
    Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253
      removed outlier: 6.312A  pdb=" N   ASN B 225 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423
      removed outlier: 8.441A  pdb=" N   THR B 420 " --> pdb=" O   GLU B 389 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   VAL B 391 " --> pdb=" O   THR B 420 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   TYR B 422 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE B 393 " --> pdb=" O   TYR B 422 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   PHE B 367 " --> pdb=" O   PRO B 390 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34
      removed outlier: 6.125A  pdb=" N   VAL C 351 " --> pdb=" O   VAL C 374 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLY C 376 " --> pdb=" O   VAL C 351 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ARG C 350 " --> pdb=" O   LEU C 420 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   GLY C 422 " --> pdb=" O   ARG C 350 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   MET C 352 " --> pdb=" O   GLY C 422 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ILE C 421 " --> pdb=" O   ARG C 439 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181
      removed outlier: 4.139A  pdb=" N   PHE C 114 " --> pdb=" O   HIS C  80 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254
      removed outlier: 7.193A  pdb=" N   ILE C 225 " --> pdb=" O   VAL C 250 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLN C 252 " --> pdb=" O   ILE C 225 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   GLY C 227 " --> pdb=" O   GLN C 252 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   SER C 254 " --> pdb=" O   GLY C 227 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ASP C 222 " --> pdb=" O   LEU C 270 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   LEU C 272 " --> pdb=" O   ASP C 222 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ALA C 224 " --> pdb=" O   LEU C 272 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ASN C 271 " --> pdb=" O   MET C 295 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115
    Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253
      removed outlier: 6.316A  pdb=" N   ASN D 225 " --> pdb=" O   VAL D 291 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423
      removed outlier: 8.433A  pdb=" N   THR D 420 " --> pdb=" O   GLU D 389 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   VAL D 391 " --> pdb=" O   THR D 420 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   TYR D 422 " --> pdb=" O   VAL D 391 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE D 393 " --> pdb=" O   TYR D 422 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   PHE D 367 " --> pdb=" O   PRO D 390 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ARG D 366 " --> pdb=" O   PHE D 441 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ILE D 443 " --> pdb=" O   ARG D 366 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ALA D 368 " --> pdb=" O   ILE D 443 " (cutoff:3.500A)

    798 hydrogen bonds defined for protein.
    2283 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.86

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.57: 16164
        1.57 -     1.92: 178
        1.92 -     2.27: 46
        2.27 -     2.61: 72
        2.61 -     2.96: 18
  Bond restraints: 16478
  Sorted by residual:
  bond pdb="FE2 BCLF B 602 "
       pdb="FE8 BCLF B 602 "
    ideal  model  delta    sigma   weight residual
    2.200  2.962 -0.762 2.00e-02 2.50e+03 1.45e+03
  bond pdb="FE2 BCLF D 601 "
       pdb="FE8 BCLF D 601 "
    ideal  model  delta    sigma   weight residual
    2.200  2.956 -0.756 2.00e-02 2.50e+03 1.43e+03
  bond pdb="FE4 BCLF D 601 "
       pdb="FE5 BCLF D 601 "
    ideal  model  delta    sigma   weight residual
    2.200  2.927 -0.727 2.00e-02 2.50e+03 1.32e+03
  bond pdb="FE4 BCLF B 602 "
       pdb="FE5 BCLF B 602 "
    ideal  model  delta    sigma   weight residual
    2.200  2.923 -0.723 2.00e-02 2.50e+03 1.31e+03
  bond pdb="FE6 BCLF B 602 "
       pdb="FE7 BCLF B 602 "
    ideal  model  delta    sigma   weight residual
    2.200  2.862 -0.662 2.00e-02 2.50e+03 1.09e+03
  ... (remaining 16473 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.87: 22220
        6.87 -    13.74: 6
       13.74 -    20.61: 2
       20.61 -    27.47: 0
       27.47 -    34.34: 4
  Bond angle restraints: 22232
  Sorted by residual:
  angle pdb=" S1 BCLF B 602 "
        pdb="FE2 BCLF B 602 "
        pdb="FE4 BCLF B 602 "
      ideal   model   delta    sigma   weight residual
      90.00   55.66   34.34 3.00e+00 1.11e-01 1.31e+02
  angle pdb=" S1 BCLF D 601 "
        pdb="FE2 BCLF D 601 "
        pdb="FE4 BCLF D 601 "
      ideal   model   delta    sigma   weight residual
      90.00   55.99   34.01 3.00e+00 1.11e-01 1.29e+02
  angle pdb=" S1 BCLF B 602 "
        pdb="FE2 BCLF B 602 "
        pdb="FE1 BCLF B 602 "
      ideal   model   delta    sigma   weight residual
      90.00   57.03   32.97 3.00e+00 1.11e-01 1.21e+02
  angle pdb=" S1 BCLF D 601 "
        pdb="FE2 BCLF D 601 "
        pdb="FE1 BCLF D 601 "
      ideal   model   delta    sigma   weight residual
      90.00   57.24   32.76 3.00e+00 1.11e-01 1.19e+02
  angle pdb=" S1 BCLF D 601 "
        pdb="FE2 BCLF D 601 "
        pdb="FE3 BCLF D 601 "
      ideal   model   delta    sigma   weight residual
      90.00  107.82  -17.82 3.00e+00 1.11e-01 3.53e+01
  ... (remaining 22227 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 8760
       17.67 -    35.35: 973
       35.35 -    53.02: 254
       53.02 -    70.70: 70
       70.70 -    88.37: 37
  Dihedral angle restraints: 10094
    sinusoidal: 4360
      harmonic: 5734
  Sorted by residual:
  dihedral pdb=" CA  GLY C 105 "
           pdb=" C   GLY C 105 "
           pdb=" N   VAL C 106 "
           pdb=" CA  VAL C 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.51  -20.49     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  GLY A 105 "
           pdb=" C   GLY A 105 "
           pdb=" N   VAL A 106 "
           pdb=" CA  VAL A 106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.84  -20.16     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  ILE C  75 "
           pdb=" C   ILE C  75 "
           pdb=" N   LYS C  76 "
           pdb=" CA  LYS C  76 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.18  -19.82     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 10091 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1222
       0.029 -    0.059: 691
       0.059 -    0.088: 255
       0.088 -    0.117: 135
       0.117 -    0.147: 31
  Chirality restraints: 2334
  Sorted by residual:
  chirality pdb=" CA  ILE B 318 "
            pdb=" N   ILE B 318 "
            pdb=" C   ILE B 318 "
            pdb=" CB  ILE B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.38e-01
  chirality pdb=" CA  ILE D 318 "
            pdb=" N   ILE D 318 "
            pdb=" C   ILE D 318 "
            pdb=" CB  ILE D 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" CA  PRO D  72 "
            pdb=" N   PRO D  72 "
            pdb=" C   PRO D  72 "
            pdb=" CB  PRO D  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.64e-01
  ... (remaining 2331 not shown)

  Planarity restraints: 2856
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 359 "    0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO A 360 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 360 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 360 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 359 "   -0.025 5.00e-02 4.00e+02   3.78e-02 2.29e+00
        pdb=" N   PRO C 360 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO C 360 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 360 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 453 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.22e+00
        pdb=" C   ARG B 453 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ARG B 453 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP B 454 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2853 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.17: 12
        2.17 -     2.85: 6236
        2.85 -     3.54: 25781
        3.54 -     4.22: 51266
        4.22 -     4.90: 81207
  Nonbonded interactions: 164502
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 109 "
            pdb="FE    FE B 603 "
     model   vdw
     1.489 2.260
  nonbonded pdb=" OD2 ASP D 357 "
            pdb=" O   HOH D 701 "
     model   vdw
     1.546 3.040
  nonbonded pdb=" OE2 GLU D 109 "
            pdb=" O   HOH D 702 "
     model   vdw
     1.838 3.040
  nonbonded pdb=" OE2 GLU B 109 "
            pdb=" O   HOH D 701 "
     model   vdw
     1.982 3.040
  nonbonded pdb="FE    FE B 603 "
            pdb=" O   HOH D 720 "
     model   vdw
     2.008 2.260
  ... (remaining 164497 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'
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'B' and resid 2 through 523)
  selection = (chain 'D' and resid 2 through 523)
}

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:             19.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     17.590
  Find NCS groups from input model:        0.690
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
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      :  0.025   0.762  16495  Z= 1.192
  Angle     :  0.749  34.342  22232  Z= 0.348
  Chirality :  0.045   0.147   2334
  Planarity :  0.004   0.044   2856
  Dihedral  : 16.924  88.372   6430
  Min Nonbonded Distance : 1.489

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 16.90 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.18), residues: 1990
  helix:  1.21 (0.16), residues: 972
  sheet: -0.40 (0.34), residues: 194
  loop : -0.48 (0.20), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 182 
 TYR   0.023   0.002   TYR A 446 
 PHE   0.014   0.002   PHE A 409 
 TRP   0.016   0.002   TRP C 335 
 HIS   0.008   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.02376 (16478)
  covalent geometry    : angle       0.74929 (22232)
  hydrogen bonds       : bond        0.13201 (  798)
  hydrogen bonds       : angle       6.78279 ( 2283)
  Misc. bond           : bond        0.18723 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.672 
Fit side-chains
REVERT: B  206 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7716 (ptp-110)
REVERT: B  400 LYS cc_start: 0.8562 (mttm) cc_final: 0.7880 (mppt)
REVERT: D  303 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8004 (mtmp)
REVERT: D  400 LYS cc_start: 0.8559 (mttm) cc_final: 0.7895 (mppt)
  outliers start: 18
  outliers final: 13
  residues processed: 193
  average time/residue: 0.8000
  time to fit residues: 168.5497
Evaluate side-chains
  195 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain B residue  206 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  377 THR
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  475 LEU
Chi-restraints excluded: chain D residue  206 ARG
Chi-restraints excluded: chain D residue  303 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 518 ASN
C 252 GLN
D 518 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.121591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.106266 restraints weight = 14568.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.01
r_work: 0.3163 rms_B_bonded: 1.37 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 2.36 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.0575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.870  16495  Z= 0.231
  Angle     :  0.743  29.058  22232  Z= 0.358
  Chirality :  0.047   0.152   2334
  Planarity :  0.005   0.058   2856
  Dihedral  :  5.981  59.475   2547
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 15.10 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.18), residues: 1990
  helix:  1.27 (0.16), residues: 980
  sheet: -0.61 (0.33), residues: 208
  loop : -0.44 (0.20), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  96 
 TYR   0.022   0.002   TYR A 446 
 PHE   0.013   0.002   PHE D  15 
 TRP   0.017   0.002   TRP C 335 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (16478)
  covalent geometry    : angle       0.74326 (22232)
  hydrogen bonds       : bond        0.05562 (  798)
  hydrogen bonds       : angle       5.81106 ( 2283)
  Misc. bond           : bond        0.23650 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 188
  time to evaluate  : 0.619 
Fit side-chains
REVERT: B   50 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7875 (mmmt)
REVERT: B  400 LYS cc_start: 0.8599 (mttm) cc_final: 0.7769 (mppt)
REVERT: C  315 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8003 (mttm)
REVERT: C  322 LYS cc_start: 0.7709 (mttp) cc_final: 0.7328 (mtpm)
REVERT: C  401 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7530 (p90)
REVERT: D  303 LYS cc_start: 0.8197 (mttp) cc_final: 0.7616 (mtmt)
REVERT: D  400 LYS cc_start: 0.8572 (mttm) cc_final: 0.7720 (mppt)
  outliers start: 39
  outliers final: 14
  residues processed: 215
  average time/residue: 0.7708
  time to fit residues: 181.5929
Evaluate side-chains
  204 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  268 GLN
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  315 LYS
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  401 TYR
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  360 THR
Chi-restraints excluded: chain D residue  369 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 145 optimal weight:    0.7980
   chunk 96 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 85 optimal weight:    0.4980
   chunk 53 optimal weight:    7.9990
   chunk 110 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   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  35 ASN
A 252 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
C 252 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.123709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.108442 restraints weight = 15101.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.04
r_work: 0.3198 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.0723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.748  16495  Z= 0.166
  Angle     :  0.688  29.151  22232  Z= 0.323
  Chirality :  0.044   0.148   2334
  Planarity :  0.004   0.047   2856
  Dihedral  :  5.481  59.702   2526
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.74 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.18), residues: 1990
  helix:  1.43 (0.16), residues: 984
  sheet: -0.59 (0.34), residues: 208
  loop : -0.40 (0.21), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  96 
 TYR   0.015   0.002   TYR A 446 
 PHE   0.012   0.001   PHE A 459 
 TRP   0.015   0.001   TRP C 335 
 HIS   0.008   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (16478)
  covalent geometry    : angle       0.68806 (22232)
  hydrogen bonds       : bond        0.04648 (  798)
  hydrogen bonds       : angle       5.58105 ( 2283)
  Misc. bond           : bond        0.19973 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 188
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A  401 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7493 (p90)
REVERT: B   50 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7823 (mmmt)
REVERT: B  400 LYS cc_start: 0.8601 (mttm) cc_final: 0.7773 (mppt)
REVERT: C  401 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7552 (p90)
REVERT: C  473 LYS cc_start: 0.8582 (mptt) cc_final: 0.8043 (mptp)
REVERT: D  303 LYS cc_start: 0.8207 (mttp) cc_final: 0.7701 (mtmm)
REVERT: D  400 LYS cc_start: 0.8570 (mttm) cc_final: 0.7714 (mppt)
  outliers start: 34
  outliers final: 14
  residues processed: 210
  average time/residue: 0.7982
  time to fit residues: 183.2636
Evaluate side-chains
  201 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 184
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  401 TYR
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  360 THR
Chi-restraints excluded: chain D residue  369 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 184 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 189 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0470
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A  98 ASN
A 252 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 ASN
C  98 ASN
C 252 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.125546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.110362 restraints weight = 15195.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.05
r_work: 0.3225 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3134
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3134
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.0892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.649  16495  Z= 0.144
  Angle     :  0.665  29.086  22232  Z= 0.309
  Chirality :  0.043   0.146   2334
  Planarity :  0.004   0.042   2856
  Dihedral  :  5.183  59.889   2522
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.80 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.18), residues: 1990
  helix:  1.56 (0.17), residues: 984
  sheet: -0.57 (0.34), residues: 208
  loop : -0.36 (0.21), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  25 
 TYR   0.013   0.001   TYR D  88 
 PHE   0.012   0.001   PHE A 459 
 TRP   0.015   0.001   TRP C 335 
 HIS   0.008   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (16478)
  covalent geometry    : angle       0.66517 (22232)
  hydrogen bonds       : bond        0.04200 (  798)
  hydrogen bonds       : angle       5.42812 ( 2283)
  Misc. bond           : bond        0.17362 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 189
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.7883 (mttp) cc_final: 0.7676 (mttt)
REVERT: A  401 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7554 (p90)
REVERT: B   50 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7806 (mmmt)
REVERT: B  400 LYS cc_start: 0.8613 (mttm) cc_final: 0.7870 (mppt)
REVERT: C  401 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7603 (p90)
REVERT: C  473 LYS cc_start: 0.8588 (mptt) cc_final: 0.8038 (mptp)
REVERT: D  303 LYS cc_start: 0.8198 (mttp) cc_final: 0.7677 (mtmt)
REVERT: D  400 LYS cc_start: 0.8575 (mttm) cc_final: 0.7716 (mppt)
  outliers start: 33
  outliers final: 14
  residues processed: 215
  average time/residue: 0.7504
  time to fit residues: 176.9147
Evaluate side-chains
  202 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  401 TYR
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain D residue  360 THR
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  436 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 131 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 172 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 182 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A  98 ASN
A 252 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
C  98 ASN
C 252 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.120751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.105248 restraints weight = 15217.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.05
r_work: 0.3153 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.0739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.864  16495  Z= 0.241
  Angle     :  0.744  29.270  22232  Z= 0.356
  Chirality :  0.048   0.153   2334
  Planarity :  0.005   0.065   2856
  Dihedral  :  5.495  58.316   2522
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.56 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.18), residues: 1990
  helix:  1.30 (0.16), residues: 986
  sheet: -0.67 (0.33), residues: 208
  loop : -0.49 (0.20), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  96 
 TYR   0.018   0.002   TYR D 142 
 PHE   0.013   0.002   PHE D 201 
 TRP   0.016   0.002   TRP C 335 
 HIS   0.009   0.002   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (16478)
  covalent geometry    : angle       0.74369 (22232)
  hydrogen bonds       : bond        0.05514 (  798)
  hydrogen bonds       : angle       5.64553 ( 2283)
  Misc. bond           : bond        0.22986 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 186
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A  401 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7550 (p90)
REVERT: B   50 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7790 (mmmt)
REVERT: B  172 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8438 (mt-10)
REVERT: B  400 LYS cc_start: 0.8558 (mttm) cc_final: 0.7684 (mppt)
REVERT: C  315 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8013 (mttm)
REVERT: C  401 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7558 (p90)
REVERT: C  473 LYS cc_start: 0.8596 (mptt) cc_final: 0.7973 (mptp)
REVERT: D  303 LYS cc_start: 0.8227 (mttp) cc_final: 0.7769 (mtmp)
REVERT: D  400 LYS cc_start: 0.8542 (mttm) cc_final: 0.7630 (mppt)
  outliers start: 40
  outliers final: 21
  residues processed: 215
  average time/residue: 0.7784
  time to fit residues: 183.2697
Evaluate side-chains
  210 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 184
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  315 LYS
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  377 THR
Chi-restraints excluded: chain C residue  401 TYR
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  360 THR
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  436 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0970
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 145 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 41 optimal weight:    0.3980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A  98 ASN
A 252 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 252 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.122668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.107338 restraints weight = 15144.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.04
r_work: 0.3183 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.0794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.772  16495  Z= 0.180
  Angle     :  0.702  29.151  22232  Z= 0.331
  Chirality :  0.045   0.147   2334
  Planarity :  0.004   0.052   2856
  Dihedral  :  5.400  59.879   2522
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.39 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.18), residues: 1990
  helix:  1.40 (0.16), residues: 984
  sheet: -0.66 (0.34), residues: 208
  loop : -0.43 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  96 
 TYR   0.015   0.002   TYR D  88 
 PHE   0.012   0.002   PHE C 459 
 TRP   0.016   0.002   TRP C 335 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (16478)
  covalent geometry    : angle       0.70233 (22232)
  hydrogen bonds       : bond        0.04823 (  798)
  hydrogen bonds       : angle       5.53806 ( 2283)
  Misc. bond           : bond        0.20518 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 185
  time to evaluate  : 0.645 
Fit side-chains
REVERT: A  401 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7587 (p90)
REVERT: B   50 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7866 (mmmt)
REVERT: B  400 LYS cc_start: 0.8606 (mttm) cc_final: 0.7774 (mppt)
REVERT: C  315 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8024 (mttm)
REVERT: C  401 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7592 (p90)
REVERT: C  473 LYS cc_start: 0.8617 (mptt) cc_final: 0.8020 (mptp)
REVERT: D  303 LYS cc_start: 0.8249 (mttp) cc_final: 0.7805 (mtmp)
REVERT: D  400 LYS cc_start: 0.8580 (mttm) cc_final: 0.7712 (mppt)
  outliers start: 35
  outliers final: 18
  residues processed: 212
  average time/residue: 0.7650
  time to fit residues: 177.4859
Evaluate side-chains
  206 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 184
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain C residue  315 LYS
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  377 THR
Chi-restraints excluded: chain C residue  401 TYR
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  360 THR
Chi-restraints excluded: chain D residue  369 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 145 optimal weight:    2.9990
   chunk 151 optimal weight:    4.9990
   chunk 75 optimal weight:    0.5980
   chunk 188 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 186 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 139 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A  98 ASN
A 252 GLN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
C  98 ASN
C 252 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.121323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.105847 restraints weight = 15212.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 1.05
r_work: 0.3161 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.0775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.840  16495  Z= 0.218
  Angle     :  0.728  29.218  22232  Z= 0.347
  Chirality :  0.047   0.150   2334
  Planarity :  0.004   0.062   2856
  Dihedral  :  5.472  58.416   2522
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.56 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.18), residues: 1990
  helix:  1.32 (0.16), residues: 984
  sheet: -0.68 (0.33), residues: 208
  loop : -0.45 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  96 
 TYR   0.017   0.002   TYR D  88 
 PHE   0.013   0.002   PHE D 201 
 TRP   0.016   0.002   TRP A 335 
 HIS   0.009   0.001   HIS D 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (16478)
  covalent geometry    : angle       0.72775 (22232)
  hydrogen bonds       : bond        0.05235 (  798)
  hydrogen bonds       : angle       5.59801 ( 2283)
  Misc. bond           : bond        0.22391 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 186
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  401 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7599 (p90)
REVERT: B   50 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7870 (mmmt)
REVERT: B  400 LYS cc_start: 0.8604 (mttm) cc_final: 0.7772 (mppt)
REVERT: C  315 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8045 (mttm)
REVERT: C  401 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7600 (p90)
REVERT: C  473 LYS cc_start: 0.8604 (mptt) cc_final: 0.7991 (mptp)
REVERT: D  303 LYS cc_start: 0.8289 (mttp) cc_final: 0.7840 (mtmp)
REVERT: D  400 LYS cc_start: 0.8582 (mttm) cc_final: 0.7717 (mppt)
  outliers start: 33
  outliers final: 23
  residues processed: 208
  average time/residue: 0.7790
  time to fit residues: 177.5770
Evaluate side-chains
  213 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 186
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  360 THR
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue  315 LYS
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  377 THR
Chi-restraints excluded: chain C residue  401 TYR
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  360 THR
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  436 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 171 optimal weight:    2.9990
   chunk 189 optimal weight:    0.0670
   chunk 131 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0030
   chunk 119 optimal weight:    0.0980
   chunk 59 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   chunk 90 optimal weight:    0.2980
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.2128

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.113617 restraints weight = 15096.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.05
r_work: 0.3269 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.559  16495  Z= 0.125
  Angle     :  0.649  29.051  22232  Z= 0.299
  Chirality :  0.042   0.142   2334
  Planarity :  0.004   0.056   2856
  Dihedral  :  5.071  59.714   2522
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 16.32 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.19), residues: 1990
  helix:  1.67 (0.17), residues: 980
  sheet: -0.47 (0.36), residues: 198
  loop : -0.31 (0.21), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  97 
 TYR   0.022   0.001   TYR A  99 
 PHE   0.016   0.001   PHE A 409 
 TRP   0.016   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (16478)
  covalent geometry    : angle       0.64884 (22232)
  hydrogen bonds       : bond        0.03664 (  798)
  hydrogen bonds       : angle       5.31292 ( 2283)
  Misc. bond           : bond        0.14839 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 203
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A  401 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7580 (p90)
REVERT: A  445 ASP cc_start: 0.8333 (m-30) cc_final: 0.7754 (m-30)
REVERT: B  400 LYS cc_start: 0.8612 (mttm) cc_final: 0.7868 (mppt)
REVERT: C  401 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7475 (p90)
REVERT: C  473 LYS cc_start: 0.8553 (mptt) cc_final: 0.7977 (mptp)
REVERT: D  303 LYS cc_start: 0.8215 (mttp) cc_final: 0.7777 (mtmp)
REVERT: D  330 MET cc_start: 0.8794 (mtm) cc_final: 0.8592 (mtp)
REVERT: D  400 LYS cc_start: 0.8578 (mttm) cc_final: 0.7713 (mppt)
  outliers start: 18
  outliers final: 9
  residues processed: 216
  average time/residue: 0.7767
  time to fit residues: 183.8163
Evaluate side-chains
  201 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 190
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  401 TYR
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  369 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 152 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 81 optimal weight:    0.5980
   chunk 42 optimal weight:    0.2980
   chunk 101 optimal weight:    3.9990
   chunk 146 optimal weight:    4.9990
   chunk 105 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 126 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.125264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.109892 restraints weight = 15459.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.06
r_work: 0.3219 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.661  16495  Z= 0.155
  Angle     :  0.677  29.128  22232  Z= 0.315
  Chirality :  0.044   0.147   2334
  Planarity :  0.004   0.054   2856
  Dihedral  :  5.121  59.327   2522
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 16.90 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.18), residues: 1990
  helix:  1.63 (0.17), residues: 986
  sheet: -0.57 (0.34), residues: 208
  loop : -0.36 (0.21), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  96 
 TYR   0.015   0.002   TYR B  88 
 PHE   0.016   0.001   PHE A 409 
 TRP   0.015   0.001   TRP C 335 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (16478)
  covalent geometry    : angle       0.67707 (22232)
  hydrogen bonds       : bond        0.04292 (  798)
  hydrogen bonds       : angle       5.34861 ( 2283)
  Misc. bond           : bond        0.17754 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 190
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.7816 (mttp) cc_final: 0.7611 (mttt)
REVERT: A  401 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7633 (p90)
REVERT: B   50 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7822 (mmmt)
REVERT: B  400 LYS cc_start: 0.8619 (mttm) cc_final: 0.7880 (mppt)
REVERT: C   15 GLU cc_start: 0.7290 (pt0) cc_final: 0.6677 (pt0)
REVERT: C  401 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7625 (p90)
REVERT: C  473 LYS cc_start: 0.8570 (mptt) cc_final: 0.7966 (mptp)
REVERT: D  303 LYS cc_start: 0.8253 (mttp) cc_final: 0.7799 (mtmp)
REVERT: D  400 LYS cc_start: 0.8595 (mttm) cc_final: 0.7725 (mppt)
  outliers start: 16
  outliers final: 11
  residues processed: 201
  average time/residue: 0.7863
  time to fit residues: 172.9008
Evaluate side-chains
  202 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 188
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  401 TYR
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  436 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 133 optimal weight:    0.9990
   chunk 118 optimal weight:    2.9990
   chunk 123 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 193 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   chunk 174 optimal weight:    0.0770
   chunk 32 optimal weight:    1.9990
   chunk 128 optimal weight:    0.3980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.8142

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A  98 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
C  98 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.123813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.108352 restraints weight = 15392.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.06
r_work: 0.3197 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.0936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.731  16495  Z= 0.173
  Angle     :  0.694  29.153  22232  Z= 0.326
  Chirality :  0.045   0.148   2334
  Planarity :  0.004   0.050   2856
  Dihedral  :  5.239  58.176   2522
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 16.90 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.18), residues: 1990
  helix:  1.54 (0.16), residues: 986
  sheet: -0.61 (0.34), residues: 208
  loop : -0.37 (0.20), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  96 
 TYR   0.015   0.002   TYR D  88 
 PHE   0.016   0.002   PHE A 409 
 TRP   0.015   0.002   TRP C 335 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (16478)
  covalent geometry    : angle       0.69442 (22232)
  hydrogen bonds       : bond        0.04611 (  798)
  hydrogen bonds       : angle       5.42735 ( 2283)
  Misc. bond           : bond        0.19526 (   17)

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

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

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3980 Ramachandran restraints generated.
    1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 190
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A   51 LYS cc_start: 0.7852 (mttp) cc_final: 0.7650 (mttt)
REVERT: A  401 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7620 (p90)
REVERT: B   50 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7864 (mmmt)
REVERT: B  400 LYS cc_start: 0.8618 (mttm) cc_final: 0.7881 (mppt)
REVERT: C   15 GLU cc_start: 0.7265 (pt0) cc_final: 0.6651 (pt0)
REVERT: C  401 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7611 (p90)
REVERT: C  473 LYS cc_start: 0.8577 (mptt) cc_final: 0.7971 (mptp)
REVERT: D  303 LYS cc_start: 0.8269 (mttp) cc_final: 0.7810 (mtmp)
REVERT: D  400 LYS cc_start: 0.8598 (mttm) cc_final: 0.7728 (mppt)
  outliers start: 16
  outliers final: 12
  residues processed: 202
  average time/residue: 0.8186
  time to fit residues: 180.1888
Evaluate side-chains
  203 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 188
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  401 TYR
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  436 THR
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  355 ILE
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain C residue  401 TYR
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  369 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 186 optimal weight:    0.6980
   chunk 151 optimal weight:    3.9990
   chunk 135 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 158 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 139 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A  98 ASN
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.123708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.108283 restraints weight = 15351.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.06
r_work: 0.3196 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.0927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.734  16495  Z= 0.215
  Angle     :  0.866  59.143  22232  Z= 0.456
  Chirality :  0.050   0.904   2334
  Planarity :  0.004   0.067   2856
  Dihedral  :  5.314  58.196   2522
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.51 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 16.84 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.18), residues: 1990
  helix:  1.53 (0.16), residues: 986
  sheet: -0.61 (0.34), residues: 208
  loop : -0.38 (0.20), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.016   0.002   TYR D  88 
 PHE   0.015   0.002   PHE A 409 
 TRP   0.015   0.002   TRP C 335 
 HIS   0.008   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (16478)
  covalent geometry    : angle       0.86612 (22232)
  hydrogen bonds       : bond        0.04681 (  798)
  hydrogen bonds       : angle       5.42758 ( 2283)
  Misc. bond           : bond        0.19600 (   17)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6335.29 seconds
wall clock time: 108 minutes 59.19 seconds (6539.19 seconds total)