Starting phenix.real_space_refine
on Mon Apr  6 07:12:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ctz_45923/04_2026/9ctz_45923.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ctz_45923/04_2026/9ctz_45923.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ctz_45923/04_2026/9ctz_45923.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ctz_45923/04_2026/9ctz_45923.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ctz_45923/04_2026/9ctz_45923.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ctz_45923/04_2026/9ctz_45923.cif"
  }
  resolution = 2.67
  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=   0.021
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     139      5.16       5
     C   10170      2.51       5
     N    2702      2.21       5
     O    3906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s

  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: 16951
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 3793
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 477, 3790
          Classifications: {'peptide': 477}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455}
      Conformer: "B"
        Number of residues, atoms: 477, 3790
          Classifications: {'peptide': 477}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455}
          bond proxies already assigned to first conformer: 3874
    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: 2
      Conformer: "A"
        Number of residues, atoms: 477, 3787
          Classifications: {'peptide': 477}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
      Conformer: "B"
        Number of residues, atoms: 477, 3787
          Classifications: {'peptide': 477}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
          bond proxies already assigned to first conformer: 3871
    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: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {' FE': 1, 'CLF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    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: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {' FE': 1, 'CLF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 227
          Classifications: {'water': 227}
          Link IDs: {None: 226}
    Chain: "B"
      Number of atoms: 237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 237
          Classifications: {'water': 237}
          Link IDs: {None: 236}
    Chain: "C"
      Number of atoms: 221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 221
          Classifications: {'water': 221}
          Link IDs: {None: 220}
    Chain: "D"
      Number of atoms: 239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 239
          Classifications: {'water': 239}
          Link IDs: {None: 238}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2092  SG  CYS A 275      31.097  44.142  58.378  1.00 74.35           S
  ATOM   4552  SG  CYS B  95      40.714  29.137  43.156  1.00 52.29           S
  ATOM   1170  SG  CYS A 154      37.260  25.809  46.230  1.00 46.60           S
  ATOM    465  SG  CYS A  62      37.761  31.863  48.481  1.00 55.76           S
  ATOM    652  SG  CYS A  88      43.366  27.528  48.403  1.00 53.29           S
  ATOM    652  SG  CYS A  88      43.366  27.528  48.403  1.00 53.29           S
  ATOM   5005  SG  CYS B 153      41.388  23.883  44.471  1.00 61.44           S
  ATOM   4372  SG  CYS B  70      47.146  28.131  43.054  1.00 40.20           S
  ATOM   4552  SG  CYS B  95      40.714  29.137  43.156  1.00 52.29           S
  ATOM  10056  SG  CYS C 275     108.541  55.840  58.373  1.00 78.10           S
  ATOM  12516  SG  CYS D  95      99.168  70.888  42.627  1.00 51.53           S
  ATOM   9134  SG  CYS C 154     102.328  74.210  46.218  1.00 48.14           S
  ATOM   8429  SG  CYS C  62     101.923  68.021  48.561  1.00 55.81           S
  ATOM   8616  SG  CYS C  88      96.358  72.597  48.227  1.00 53.52           S
  ATOM   8616  SG  CYS C  88      96.358  72.597  48.227  1.00 53.52           S
  ATOM  12969  SG  CYS D 153      98.196  75.939  44.419  1.00 62.49           S
  ATOM  12336  SG  CYS D  70      92.537  71.853  43.021  1.00 42.24           S
  ATOM  12516  SG  CYS D  95      99.168  70.888  42.627  1.00 51.53           S

  Time building chain proxies: 5.15, per 1000 atoms: 0.30
  Number of scatterers: 16951
  At special positions: 0
  Unit cell: (138.18, 100.695, 98.49, 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     139     16.00
     O    3906      8.00
     N    2702      7.00
     C   10170      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=16, symmetry=0
  Number of additional bonds: simple=16, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.28
  Conformation dependent library (CDL) restraints added in 850.0 milliseconds
  

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3668

  Finding SS restraints...
    Secondary structure from input PDB file:
      102 helices and 12 sheets defined
      58.2% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 18
    Processing helix  chain 'A' and resid 21 through 30
      removed outlier: 4.191A  pdb=" N   LYS A  30 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 3.809A  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 153 through 159
      removed outlier: 3.563A  pdb=" N   GLY A 157 " --> pdb=" O   GLU A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 175
      removed outlier: 4.028A  pdb=" N   VAL A 166 " --> pdb=" O   ASP A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 206
      removed outlier: 4.218A  pdb=" N   GLY A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 211
      removed outlier: 4.468A  pdb=" N   ARG A 210 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP A 211 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 207 through 211'
    Processing helix  chain 'A' and resid 230 through 232
      No H-bonds generated for 'chain 'A' and resid 230 through 232'
    Processing helix  chain 'A' and resid 233 through 245
      removed outlier: 4.324A  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: 5.804A  pdb=" N   TYR A 281 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 5.690A  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
      removed outlier: 3.517A  pdb=" N   HIS A 362 " --> pdb=" O   LEU A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 370
    Processing helix  chain 'A' and resid 383 through 394
    Processing helix  chain 'A' and resid 405 through 417
    Processing helix  chain 'A' and resid 424 through 434
      removed outlier: 4.352A  pdb=" N   PHE A 429 " --> pdb=" O   ILE A 425 " (cutoff:3.500A)
      removed outlier: 5.200A  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
      removed outlier: 3.672A  pdb=" N   ALA A 457 " --> pdb=" O   PHE A 453 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE A 458 " --> pdb=" O   ASP A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 474
      removed outlier: 3.509A  pdb=" N   TRP A 472 " --> pdb=" O   ASN A 469 " (cutoff:3.500A)
    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 57
    Processing helix  chain 'B' and resid 70 through 80
      removed outlier: 4.024A  pdb=" N   GLY B  74 " --> pdb=" O   CYS B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 108
      removed outlier: 4.253A  pdb=" N   VAL B  96 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
    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 173
    Processing helix  chain 'B' and resid 192 through 210
    Processing helix  chain 'B' and resid 233 through 247
      removed outlier: 3.804A  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 320 through 337
      removed outlier: 4.187A  pdb=" N   TRP B 324 " --> pdb=" O   MET B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 363
      removed outlier: 3.591A  pdb=" N   THR B 345 " --> pdb=" O   PRO B 341 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   THR B 360 " --> pdb=" O   THR B 356 " (cutoff:3.500A)
      removed outlier: 5.704A  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: 3.730A  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: 4.438A  pdb=" N   ILE B 451 " --> pdb=" O   TYR B 447 " (cutoff:3.500A)
    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: 4.208A  pdb=" N   LYS C  30 " --> pdb=" O   LYS C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 45
      removed outlier: 3.513A  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 125
    Processing helix  chain 'C' and resid 127 through 142
    Processing helix  chain 'C' and resid 153 through 160
      removed outlier: 3.501A  pdb=" N   GLY C 157 " --> pdb=" O   GLU C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 175
      removed outlier: 3.645A  pdb=" N   VAL C 166 " --> pdb=" O   ASP C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 206
      removed outlier: 4.226A  pdb=" N   GLY C 194 " --> pdb=" O   SER C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 211
      removed outlier: 4.415A  pdb=" N   ARG C 210 " --> pdb=" O   LEU C 207 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASP C 211 " --> pdb=" O   GLY C 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 207 through 211'
    Processing helix  chain 'C' and resid 230 through 232
      No H-bonds generated for 'chain 'C' and resid 230 through 232'
    Processing helix  chain 'C' and resid 233 through 245
      removed outlier: 4.366A  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 290
      removed outlier: 5.784A  pdb=" N   TYR C 281 " --> pdb=" O   ARG C 277 " (cutoff:3.500A)
      removed outlier: 5.672A  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
      removed outlier: 3.516A  pdb=" N   GLN C 321 " --> pdb=" O   ASP C 317 " (cutoff:3.500A)
      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 370
    Processing helix  chain 'C' and resid 383 through 392
      removed outlier: 4.046A  pdb=" N   LYS C 392 " --> pdb=" O   ASP C 388 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 417
    Processing helix  chain 'C' and resid 424 through 434
      removed outlier: 4.416A  pdb=" N   PHE C 429 " --> pdb=" O   ILE C 425 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   ILE C 430 " --> pdb=" O   LYS C 426 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 451 through 468
      removed outlier: 3.640A  pdb=" N   ALA C 457 " --> pdb=" O   PHE C 453 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ILE C 458 " --> pdb=" O   ASP C 454 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 469 through 474
      removed outlier: 3.512A  pdb=" N   TRP C 472 " --> pdb=" O   ASN C 469 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 15
    Processing helix  chain 'D' and resid 17 through 32
      removed outlier: 3.631A  pdb=" N   GLU D  32 " --> pdb=" O   ARG D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 47
    Processing helix  chain 'D' and resid 49 through 58
    Processing helix  chain 'D' and resid 70 through 80
      removed outlier: 4.005A  pdb=" N   GLY D  74 " --> pdb=" O   CYS D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 108
      removed outlier: 4.059A  pdb=" N   VAL D  96 " --> pdb=" O   SER D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 126
    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 233 through 247
      removed outlier: 3.849A  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: 3.575A  pdb=" N   THR D 345 " --> pdb=" O   PRO D 341 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   THR D 360 " --> pdb=" O   THR D 356 " (cutoff:3.500A)
      removed outlier: 5.694A  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: 3.823A  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: 4.407A  pdb=" N   ILE D 451 " --> pdb=" O   TYR D 447 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 478 through 482
      removed outlier: 3.571A  pdb=" N   ARG D 481 " --> pdb=" O   HIS D 478 " (cutoff:3.500A)
    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: 6.115A  pdb=" N   VAL A 351 " --> pdb=" O   VAL A 374 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY A 376 " --> pdb=" O   VAL A 351 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ARG A 350 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   GLY A 422 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   MET A 352 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
      removed outlier: 6.321A  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: 6.952A  pdb=" N   ILE A 148 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   VAL A 150 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 4.298A  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: 6.675A  pdb=" N   VAL A 223 " --> pdb=" O   CYS A 249 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ALA A 251 " --> pdb=" O   VAL A 223 " (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: 6.385A  pdb=" N   ILE B 224 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   ASN B 225 " --> pdb=" O   VAL B 291 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423
      removed outlier: 8.543A  pdb=" N   THR B 420 " --> pdb=" O   GLU B 389 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   VAL B 391 " --> pdb=" O   THR B 420 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   TYR B 422 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ILE B 393 " --> pdb=" O   TYR B 422 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   PHE B 367 " --> pdb=" O   PRO B 390 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   HIS B 392 " --> pdb=" O   PHE B 367 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34
      removed outlier: 7.583A  pdb=" N   VAL C 351 " --> pdb=" O   VAL C 375 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   THR C 377 " --> pdb=" O   VAL C 351 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   LEU C 353 " --> pdb=" O   THR C 377 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   TYR C 379 " --> pdb=" O   LEU C 353 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ARG C 350 " --> pdb=" O   LEU C 420 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   GLY C 422 " --> pdb=" O   ARG C 350 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   MET C 352 " --> pdb=" O   GLY C 422 " (cutoff:3.500A)
      removed outlier: 6.322A  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: 6.946A  pdb=" N   ILE C 148 " --> pdb=" O   VAL C 179 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   VAL C 181 " --> pdb=" O   ILE C 148 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   VAL C 150 " --> pdb=" O   VAL C 181 " (cutoff:3.500A)
      removed outlier: 4.290A  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: 7.373A  pdb=" N   VAL C 223 " --> pdb=" O   ALA C 251 " (cutoff:3.500A)
      removed outlier: 8.870A  pdb=" N   TRP C 253 " --> pdb=" O   VAL C 223 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ILE C 225 " --> pdb=" O   TRP C 253 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU C 270 " --> pdb=" O   ASP C 222 " (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: 6.302A  pdb=" N   ILE D 224 " --> pdb=" O   SER D 252 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASN D 225 " --> pdb=" O   VAL D 291 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423
      removed outlier: 8.805A  pdb=" N   THR D 420 " --> pdb=" O   GLU D 389 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   VAL D 391 " --> pdb=" O   THR D 420 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   TYR D 422 " --> pdb=" O   VAL D 391 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ILE D 393 " --> pdb=" O   TYR D 422 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   PHE D 367 " --> pdb=" O   PRO D 390 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   HIS D 392 " --> pdb=" O   PHE D 367 " (cutoff:3.500A)

    784 hydrogen bonds defined for protein.
    2274 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: 3.15

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.86: 16347
        1.86 -     2.49: 105
        2.49 -     3.13: 19
        3.13 -     3.76: 8
        3.76 -     4.40: 4
  Bond restraints: 16483
  Sorted by residual:
  bond pdb="FE2  CLF B 602 "
       pdb="FE8  CLF B 602 "
    ideal  model  delta    sigma   weight residual
    2.200  4.397 -2.197 2.00e-02 2.50e+03 1.21e+04
  bond pdb="FE2  CLF D 602 "
       pdb="FE8  CLF D 602 "
    ideal  model  delta    sigma   weight residual
    2.200  4.396 -2.196 2.00e-02 2.50e+03 1.21e+04
  bond pdb="FE5  CLF D 602 "
       pdb="FE6  CLF D 602 "
    ideal  model  delta    sigma   weight residual
    2.200  3.904 -1.704 2.00e-02 2.50e+03 7.26e+03
  bond pdb="FE5  CLF B 602 "
       pdb="FE6  CLF B 602 "
    ideal  model  delta    sigma   weight residual
    2.200  3.903 -1.703 2.00e-02 2.50e+03 7.25e+03
  bond pdb="FE4  CLF B 602 "
       pdb="FE5  CLF B 602 "
    ideal  model  delta    sigma   weight residual
    2.200  3.617 -1.417 2.00e-02 2.50e+03 5.02e+03
  ... (remaining 16478 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.79: 22236
        6.79 -    13.57: 1
       13.57 -    20.36: 2
       20.36 -    27.14: 0
       27.14 -    33.93: 4
  Bond angle restraints: 22243
  Sorted by residual:
  angle pdb=" S1  CLF D 602 "
        pdb="FE2  CLF D 602 "
        pdb="FE4  CLF D 602 "
      ideal   model   delta    sigma   weight residual
      90.00   56.07   33.93 3.00e+00 1.11e-01 1.28e+02
  angle pdb=" S1  CLF B 602 "
        pdb="FE2  CLF B 602 "
        pdb="FE4  CLF B 602 "
      ideal   model   delta    sigma   weight residual
      90.00   56.10   33.90 3.00e+00 1.11e-01 1.28e+02
  angle pdb=" S1  CLF D 602 "
        pdb="FE2  CLF D 602 "
        pdb="FE1  CLF D 602 "
      ideal   model   delta    sigma   weight residual
      90.00   60.62   29.38 3.00e+00 1.11e-01 9.59e+01
  angle pdb=" S1  CLF B 602 "
        pdb="FE2  CLF B 602 "
        pdb="FE1  CLF B 602 "
      ideal   model   delta    sigma   weight residual
      90.00   61.19   28.81 3.00e+00 1.11e-01 9.22e+01
  angle pdb=" S1  CLF D 602 "
        pdb="FE2  CLF D 602 "
        pdb="FE3  CLF D 602 "
      ideal   model   delta    sigma   weight residual
      90.00  108.69  -18.69 3.00e+00 1.11e-01 3.88e+01
  ... (remaining 22238 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 8715
       17.89 -    35.78: 984
       35.78 -    53.67: 303
       53.67 -    71.56: 73
       71.56 -    89.45: 26
  Dihedral angle restraints: 10101
    sinusoidal: 4359
      harmonic: 5742
  Sorted by residual:
  dihedral pdb=" CD  ARG D 242 "
           pdb=" NE  ARG D 242 "
           pdb=" CZ  ARG D 242 "
           pdb=" NH1 ARG D 242 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.05  -89.05     1      1.00e+01 1.00e-02 9.44e+01
  dihedral pdb=" CD  ARG C  96 "
           pdb=" NE  ARG C  96 "
           pdb=" CZ  ARG C  96 "
           pdb=" NH1 ARG C  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.56   82.56     1      1.00e+01 1.00e-02 8.36e+01
  dihedral pdb=" CA  PHE B 367 "
           pdb=" C   PHE B 367 "
           pdb=" N   ALA B 368 "
           pdb=" CA  ALA B 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.09   21.91     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 10098 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1716
       0.046 -    0.092: 434
       0.092 -    0.138: 166
       0.138 -    0.184: 13
       0.184 -    0.230: 7
  Chirality restraints: 2336
  Sorted by residual:
  chirality pdb=" CA  PRO A 360 "
            pdb=" N   PRO A 360 "
            pdb=" C   PRO A 360 "
            pdb=" CB  PRO A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  ILE D 175 "
            pdb=" N   ILE D 175 "
            pdb=" C   ILE D 175 "
            pdb=" CB  ILE D 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  VAL B 434 "
            pdb=" CA  VAL B 434 "
            pdb=" CG1 VAL B 434 "
            pdb=" CG2 VAL B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.68e-01
  ... (remaining 2333 not shown)

  Planarity restraints: 2858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 242 "   -1.115 9.50e-02 1.11e+02   5.00e-01 1.51e+02
        pdb=" NE  ARG D 242 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 242 "    0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 242 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 242 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  96 "    1.096 9.50e-02 1.11e+02   4.91e-01 1.45e+02
        pdb=" NE  ARG C  96 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  96 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  96 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  96 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  96 "   -0.543 9.50e-02 1.11e+02   2.43e-01 3.62e+01
        pdb=" NE  ARG A  96 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  96 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  96 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  96 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 2855 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 431
        2.64 -     3.20: 14897
        3.20 -     3.77: 28633
        3.77 -     4.33: 43290
        4.33 -     4.90: 67873
  Nonbonded interactions: 155124
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D 353 "
            pdb="FE    FE D 601 "
     model   vdw
     2.070 2.260
  nonbonded pdb=" OD2 ASP B 353 "
            pdb="FE    FE B 601 "
     model   vdw
     2.078 2.260
  nonbonded pdb=" OG1 THR D 119 "
            pdb=" OD1 ASP D 121 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OG1 THR B 119 "
            pdb=" OD1 ASP B 121 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" O   LYS C  51 "
            pdb=" O   HOH C 601 "
     model   vdw
     2.186 3.040
  ... (remaining 155119 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 5 through 248 or resid 250 through 502))
  selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 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:             4.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     17.470
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
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      :  0.045   2.197  16499  Z= 2.296
  Angle     :  0.762  33.925  22243  Z= 0.406
  Chirality :  0.047   0.230   2336
  Planarity :  0.016   0.500   2858
  Dihedral  : 17.122  89.452   6433
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 19.73 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  0.40 (0.18), residues: 1992
  helix:  1.28 (0.17), residues: 978
  sheet: -0.43 (0.38), residues: 174
  loop : -0.75 (0.20), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 401 
 TYR   0.014   0.001   TYR D 142 
 PHE   0.014   0.001   PHE C 429 
 TRP   0.013   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.04476 (16483)
  covalent geometry    : angle       0.76206 (22243)
  hydrogen bonds       : bond        0.14493 (  784)
  hydrogen bonds       : angle       6.74707 ( 2274)
  Misc. bond           : bond        0.16462 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: A  300 PHE cc_start: 0.6662 (m-80) cc_final: 0.6138 (t80)
REVERT: A  332 LYS cc_start: 0.7632 (tttt) cc_final: 0.6723 (tttm)
REVERT: B   93 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.6890 (tp40)
REVERT: B  172 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6825 (mp0)
REVERT: C  287 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7133 (tm-30)
REVERT: C  300 PHE cc_start: 0.6860 (m-80) cc_final: 0.6216 (t80)
REVERT: C  332 LYS cc_start: 0.7596 (tttt) cc_final: 0.6677 (tttm)
REVERT: C  373 GLU cc_start: 0.7484 (mp0) cc_final: 0.6948 (pm20)
REVERT: C  391 MET cc_start: 0.5949 (mtt) cc_final: 0.5710 (mtp)
REVERT: D  172 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6755 (mp0)
  outliers start: 20
  outliers final: 6
  residues processed: 169
  average time/residue: 0.7103
  time to fit residues: 131.8761
Evaluate side-chains
  162 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue   92 SER
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  287 GLU
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue  172 GLU
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:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    7.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 384 ASN
A 451 HIS
B   4 GLN
B 104 ASN
B 185 HIS
D   4 GLN
D 104 ASN
D 128 GLN
D 185 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.125956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.105134 restraints weight = 18153.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.38
r_work: 0.3147 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.0783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.277  16499  Z= 0.235
  Angle     :  0.695  30.756  22243  Z= 0.322
  Chirality :  0.044   0.133   2336
  Planarity :  0.005   0.125   2858
  Dihedral  :  5.523  81.820   2538
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.35 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  0.52 (0.18), residues: 1992
  helix:  1.29 (0.16), residues: 1016
  sheet: -0.48 (0.38), residues: 176
  loop : -0.63 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  97 
 TYR   0.012   0.001   TYR A 387 
 PHE   0.010   0.001   PHE D  44 
 TRP   0.015   0.001   TRP A 253 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (16483)
  covalent geometry    : angle       0.69517 (22243)
  hydrogen bonds       : bond        0.04511 (  784)
  hydrogen bonds       : angle       5.43617 ( 2274)
  Misc. bond           : bond        0.12835 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 156
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7447 (tt0)
REVERT: A  332 LYS cc_start: 0.7724 (tttt) cc_final: 0.6893 (tttm)
REVERT: A  388 ASP cc_start: 0.6100 (m-30) cc_final: 0.5898 (m-30)
REVERT: B  172 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6454 (mp0)
REVERT: B  268 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7991 (mt0)
REVERT: C  129 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7610 (mttp)
REVERT: C  300 PHE cc_start: 0.6570 (m-80) cc_final: 0.6146 (t80)
REVERT: C  332 LYS cc_start: 0.7658 (tttt) cc_final: 0.6816 (tttm)
REVERT: C  373 GLU cc_start: 0.7355 (mp0) cc_final: 0.6993 (pm20)
REVERT: C  391 MET cc_start: 0.6219 (mtt) cc_final: 0.5950 (mtp)
REVERT: D  172 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6634 (mp0)
  outliers start: 45
  outliers final: 14
  residues processed: 190
  average time/residue: 0.7458
  time to fit residues: 155.3391
Evaluate side-chains
  168 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  268 GLN
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue   92 SER
Chi-restraints excluded: chain D residue  172 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 114 optimal weight:   10.0000
   chunk 132 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 177 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 43 optimal weight:    0.3980
   chunk 24 optimal weight:    7.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B   4 GLN
D   4 GLN
D 128 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.125739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.104941 restraints weight = 18220.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.38
r_work: 0.3130 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.262  16499  Z= 0.216
  Angle     :  0.672  30.613  22243  Z= 0.307
  Chirality :  0.044   0.163   2336
  Planarity :  0.004   0.065   2858
  Dihedral  :  5.050  63.866   2530
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.41 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  0.61 (0.18), residues: 1992
  helix:  1.40 (0.16), residues: 1016
  sheet: -0.52 (0.38), residues: 176
  loop : -0.62 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  96 
 TYR   0.012   0.001   TYR A 387 
 PHE   0.011   0.001   PHE C 409 
 TRP   0.015   0.001   TRP A 253 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (16483)
  covalent geometry    : angle       0.67186 (22243)
  hydrogen bonds       : bond        0.04137 (  784)
  hydrogen bonds       : angle       5.20681 ( 2274)
  Misc. bond           : bond        0.11983 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 157
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A  119 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.6147 (mp10)
REVERT: A  120 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7472 (tt0)
REVERT: A  300 PHE cc_start: 0.6710 (m-80) cc_final: 0.6270 (t80)
REVERT: A  332 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.6942 (tttm)
REVERT: A  417 LYS cc_start: 0.7274 (mttp) cc_final: 0.6883 (mttp)
REVERT: B  143 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8356 (mppt)
REVERT: B  172 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6482 (mp0)
REVERT: C   10 GLU cc_start: 0.6649 (mm-30) cc_final: 0.6330 (tp30)
REVERT: C  300 PHE cc_start: 0.6741 (m-80) cc_final: 0.6281 (t80)
REVERT: C  332 LYS cc_start: 0.7756 (tttt) cc_final: 0.6903 (tttm)
REVERT: C  373 GLU cc_start: 0.7329 (mp0) cc_final: 0.6984 (pm20)
REVERT: C  391 MET cc_start: 0.6259 (mtt) cc_final: 0.6005 (mtp)
REVERT: C  417 LYS cc_start: 0.7391 (mttp) cc_final: 0.6914 (mttp)
REVERT: D  172 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.6679 (mp0)
  outliers start: 43
  outliers final: 18
  residues processed: 185
  average time/residue: 0.7420
  time to fit residues: 150.6199
Evaluate side-chains
  170 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  143 LYS
Chi-restraints excluded: chain B residue  153 CYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  153 CYS
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  177 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 183 optimal weight:    0.7980
   chunk 86 optimal weight:    0.4980
   chunk 104 optimal weight:    0.7980
   chunk 60 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 153 optimal weight:    0.9980
   chunk 168 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 173 optimal weight:    0.1980
   chunk 12 optimal weight:    6.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B   4 GLN
D   4 GLN
D 128 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.127241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.105162 restraints weight = 24516.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.65
r_work: 0.3132 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.231  16499  Z= 0.196
  Angle     :  0.653  30.630  22243  Z= 0.295
  Chirality :  0.043   0.144   2336
  Planarity :  0.004   0.045   2858
  Dihedral  :  4.907  65.180   2530
  Min Nonbonded Distance : 1.785

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 18.22 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  0.81 (0.19), residues: 1992
  helix:  1.58 (0.17), residues: 1010
  sheet: -0.52 (0.38), residues: 176
  loop : -0.50 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  96 
 TYR   0.011   0.001   TYR D  88 
 PHE   0.008   0.001   PHE A 431 
 TRP   0.014   0.001   TRP A 253 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (16483)
  covalent geometry    : angle       0.65285 (22243)
  hydrogen bonds       : bond        0.03657 (  784)
  hydrogen bonds       : angle       5.04782 ( 2274)
  Misc. bond           : bond        0.10604 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 155
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.6182 (mp10)
REVERT: A  120 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7520 (tt0)
REVERT: A  300 PHE cc_start: 0.6742 (m-80) cc_final: 0.6312 (t80)
REVERT: A  332 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.6930 (tttm)
REVERT: A  417 LYS cc_start: 0.7325 (mttp) cc_final: 0.6937 (mttp)
REVERT: B  143 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8383 (mppt)
REVERT: B  172 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6153 (mp0)
REVERT: C   10 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6303 (tp30)
REVERT: C  129 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7601 (mttp)
REVERT: C  300 PHE cc_start: 0.6670 (m-80) cc_final: 0.6245 (t80)
REVERT: C  332 LYS cc_start: 0.7731 (tttt) cc_final: 0.6870 (tttm)
REVERT: C  373 GLU cc_start: 0.7325 (mp0) cc_final: 0.7027 (pm20)
REVERT: C  391 MET cc_start: 0.6214 (mtt) cc_final: 0.5957 (mtp)
REVERT: C  417 LYS cc_start: 0.7411 (mttp) cc_final: 0.6942 (mttp)
REVERT: D  172 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6637 (mp0)
REVERT: D  258 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7737 (pt0)
  outliers start: 32
  outliers final: 13
  residues processed: 178
  average time/residue: 0.7360
  time to fit residues: 143.6002
Evaluate side-chains
  167 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  143 LYS
Chi-restraints excluded: chain B residue  153 CYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  153 CYS
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  258 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 153 optimal weight:    0.9980
   chunk 181 optimal weight:    6.9990
   chunk 139 optimal weight:    0.7980
   chunk 129 optimal weight:    0.9990
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:    0.8980
   chunk 101 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  98 ASN
B   4 GLN
D   4 GLN
D 128 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.125280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.102609 restraints weight = 28300.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 1.79
r_work: 0.3089 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2962
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.237  16499  Z= 0.214
  Angle     :  0.667  30.633  22243  Z= 0.303
  Chirality :  0.044   0.133   2336
  Planarity :  0.004   0.045   2858
  Dihedral  :  5.006  65.553   2530
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.51 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  0.77 (0.19), residues: 1992
  helix:  1.57 (0.17), residues: 1008
  sheet: -0.57 (0.38), residues: 176
  loop : -0.53 (0.20), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  96 
 TYR   0.013   0.001   TYR B  88 
 PHE   0.015   0.001   PHE A 409 
 TRP   0.014   0.001   TRP A 253 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (16483)
  covalent geometry    : angle       0.66671 (22243)
  hydrogen bonds       : bond        0.04037 (  784)
  hydrogen bonds       : angle       5.07032 ( 2274)
  Misc. bond           : bond        0.11040 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 155
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6216 (mp10)
REVERT: A  120 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7605 (tt0)
REVERT: A  300 PHE cc_start: 0.6891 (m-80) cc_final: 0.6535 (t80)
REVERT: A  332 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7081 (tttm)
REVERT: A  417 LYS cc_start: 0.7343 (mttp) cc_final: 0.6966 (mttp)
REVERT: A  476 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7508 (tp40)
REVERT: B  143 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8403 (mppt)
REVERT: B  172 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6065 (mp0)
REVERT: B  268 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7953 (mt0)
REVERT: C   10 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6277 (tp30)
REVERT: C  287 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7010 (tm-30)
REVERT: C  300 PHE cc_start: 0.6742 (m-80) cc_final: 0.6357 (t80)
REVERT: C  322 LYS cc_start: 0.7283 (tttm) cc_final: 0.7077 (ttpt)
REVERT: C  332 LYS cc_start: 0.7809 (tttt) cc_final: 0.7009 (tttm)
REVERT: C  334 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7652 (mt-10)
REVERT: C  373 GLU cc_start: 0.7399 (mp0) cc_final: 0.7102 (pm20)
REVERT: C  391 MET cc_start: 0.6270 (mtt) cc_final: 0.6017 (mtp)
REVERT: C  392 LYS cc_start: 0.7041 (ttpt) cc_final: 0.6761 (tttt)
REVERT: C  417 LYS cc_start: 0.7440 (mttp) cc_final: 0.7007 (mttp)
REVERT: D  172 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6662 (mp0)
  outliers start: 37
  outliers final: 20
  residues processed: 180
  average time/residue: 0.7665
  time to fit residues: 150.8357
Evaluate side-chains
  175 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain A residue  476 GLN
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  143 LYS
Chi-restraints excluded: chain B residue  153 CYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  177 ASP
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  268 GLN
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  287 GLU
Chi-restraints excluded: chain C residue  334 GLU
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  153 CYS
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain D residue  394 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 188 optimal weight:    5.9990
   chunk 156 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 170 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 176 optimal weight:    0.7980
   chunk 179 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 145 optimal weight:    1.9990
   chunk 167 optimal weight:    3.9990
   chunk 165 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B   4 GLN
D   4 GLN
D 128 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.124602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.103869 restraints weight = 17811.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.37
r_work: 0.3122 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.240  16499  Z= 0.219
  Angle     :  0.672  30.624  22243  Z= 0.306
  Chirality :  0.044   0.133   2336
  Planarity :  0.004   0.045   2858
  Dihedral  :  4.992  65.794   2530
  Min Nonbonded Distance : 1.807

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.22 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  0.77 (0.19), residues: 1992
  helix:  1.57 (0.16), residues: 1008
  sheet: -0.60 (0.38), residues: 176
  loop : -0.54 (0.20), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  96 
 TYR   0.013   0.001   TYR B  88 
 PHE   0.011   0.001   PHE A 429 
 TRP   0.015   0.001   TRP A 253 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (16483)
  covalent geometry    : angle       0.67168 (22243)
  hydrogen bonds       : bond        0.04142 (  784)
  hydrogen bonds       : angle       5.06149 ( 2274)
  Misc. bond           : bond        0.11270 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 146
  time to evaluate  : 0.593 
Fit side-chains
REVERT: A  119 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.6168 (mp10)
REVERT: A  120 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7539 (tt0)
REVERT: A  300 PHE cc_start: 0.6901 (m-80) cc_final: 0.6571 (t80)
REVERT: A  332 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7037 (tttm)
REVERT: A  417 LYS cc_start: 0.7347 (mttp) cc_final: 0.6984 (mttp)
REVERT: B  143 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8379 (mppt)
REVERT: B  172 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.5856 (mp0)
REVERT: C   10 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6267 (tp30)
REVERT: C  287 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.6920 (tm-30)
REVERT: C  300 PHE cc_start: 0.6780 (m-80) cc_final: 0.6420 (t80)
REVERT: C  332 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7009 (tttm)
REVERT: C  334 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7567 (mt-10)
REVERT: C  373 GLU cc_start: 0.7337 (mp0) cc_final: 0.7044 (pm20)
REVERT: C  391 MET cc_start: 0.6340 (mtt) cc_final: 0.6071 (mtp)
REVERT: C  392 LYS cc_start: 0.7021 (ttpt) cc_final: 0.6769 (tttt)
REVERT: C  417 LYS cc_start: 0.7416 (mttp) cc_final: 0.6974 (mttp)
REVERT: D  172 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6534 (mp0)
  outliers start: 43
  outliers final: 22
  residues processed: 174
  average time/residue: 0.7474
  time to fit residues: 142.5406
Evaluate side-chains
  175 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  143 LYS
Chi-restraints excluded: chain B residue  153 CYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  377 MET
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  287 GLU
Chi-restraints excluded: chain C residue  332 LYS
Chi-restraints excluded: chain C residue  334 GLU
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  153 CYS
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain D residue  376 VAL
Chi-restraints excluded: chain D residue  394 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 137 optimal weight:    9.9990
   chunk 30 optimal weight:    0.8980
   chunk 158 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 140 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B   4 GLN
D   4 GLN
D 128 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.125777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.103912 restraints weight = 23348.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.61
r_work: 0.3118 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227  16499  Z= 0.202
  Angle     :  0.658  30.606  22243  Z= 0.298
  Chirality :  0.043   0.183   2336
  Planarity :  0.004   0.045   2858
  Dihedral  :  4.883  66.359   2530
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.69 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  0.85 (0.19), residues: 1992
  helix:  1.65 (0.17), residues: 1008
  sheet: -0.59 (0.38), residues: 176
  loop : -0.52 (0.21), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  96 
 TYR   0.012   0.001   TYR D  88 
 PHE   0.017   0.001   PHE A 409 
 TRP   0.014   0.001   TRP A 253 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (16483)
  covalent geometry    : angle       0.65767 (22243)
  hydrogen bonds       : bond        0.03787 (  784)
  hydrogen bonds       : angle       4.99781 ( 2274)
  Misc. bond           : bond        0.10561 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 150
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.6194 (mp10)
REVERT: A  120 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7581 (tt0)
REVERT: A  300 PHE cc_start: 0.6930 (m-80) cc_final: 0.6551 (t80)
REVERT: A  332 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7071 (tttm)
REVERT: A  417 LYS cc_start: 0.7383 (mttp) cc_final: 0.7035 (mttp)
REVERT: B  143 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8411 (mppt)
REVERT: B  268 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7911 (mt0)
REVERT: C   10 GLU cc_start: 0.6576 (mm-30) cc_final: 0.6244 (tp30)
REVERT: C  300 PHE cc_start: 0.6819 (m-80) cc_final: 0.6428 (t80)
REVERT: C  332 LYS cc_start: 0.7847 (tttt) cc_final: 0.7041 (tttm)
REVERT: C  334 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7602 (mt-10)
REVERT: C  373 GLU cc_start: 0.7335 (mp0) cc_final: 0.7064 (pm20)
REVERT: C  391 MET cc_start: 0.6377 (mtt) cc_final: 0.6115 (mtp)
REVERT: C  392 LYS cc_start: 0.6989 (ttpt) cc_final: 0.6711 (tttt)
REVERT: C  417 LYS cc_start: 0.7529 (mttp) cc_final: 0.7107 (mttp)
REVERT: D  172 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6609 (mp0)
REVERT: D  258 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7779 (pt0)
  outliers start: 40
  outliers final: 23
  residues processed: 177
  average time/residue: 0.7279
  time to fit residues: 141.0715
Evaluate side-chains
  175 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  143 LYS
Chi-restraints excluded: chain B residue  153 CYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  268 GLN
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  116 SER
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  334 GLU
Chi-restraints excluded: chain C residue  351 VAL
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  153 CYS
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain D residue  376 VAL
Chi-restraints excluded: chain D residue  377 MET
Chi-restraints excluded: chain D residue  394 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 170 optimal weight:    3.9990
   chunk 165 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0870
   chunk 34 optimal weight:    8.9990
   chunk 134 optimal weight:    0.9990
   chunk 191 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 121 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0170
   chunk 102 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
B   4 GLN
D   4 GLN
D 168 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.127397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.103861 restraints weight = 34944.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.04
r_work: 0.3100 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.210  16499  Z= 0.189
  Angle     :  0.646  30.583  22243  Z= 0.291
  Chirality :  0.042   0.181   2336
  Planarity :  0.004   0.044   2858
  Dihedral  :  4.743  66.855   2530
  Min Nonbonded Distance : 1.772

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.92 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  0.96 (0.19), residues: 1992
  helix:  1.74 (0.17), residues: 1010
  sheet: -0.54 (0.38), residues: 176
  loop : -0.47 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 359 
 TYR   0.012   0.001   TYR A 387 
 PHE   0.013   0.001   PHE A 409 
 TRP   0.013   0.001   TRP A 335 
 HIS   0.009   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (16483)
  covalent geometry    : angle       0.64638 (22243)
  hydrogen bonds       : bond        0.03452 (  784)
  hydrogen bonds       : angle       4.91092 ( 2274)
  Misc. bond           : bond        0.09724 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 151
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  119 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6182 (mp10)
REVERT: A  120 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7625 (tt0)
REVERT: A  300 PHE cc_start: 0.6853 (m-80) cc_final: 0.6499 (t80)
REVERT: A  332 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.6998 (tttm)
REVERT: A  417 LYS cc_start: 0.7344 (mttp) cc_final: 0.6997 (mttp)
REVERT: B  143 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8285 (mppt)
REVERT: B  172 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.5650 (mp0)
REVERT: C   10 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6189 (tp30)
REVERT: C   59 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8048 (mm)
REVERT: C  300 PHE cc_start: 0.6766 (m-80) cc_final: 0.6280 (t80)
REVERT: C  332 LYS cc_start: 0.7775 (tttt) cc_final: 0.6962 (tttm)
REVERT: C  334 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7603 (mt-10)
REVERT: C  373 GLU cc_start: 0.7319 (mp0) cc_final: 0.7055 (pm20)
REVERT: C  391 MET cc_start: 0.6295 (mtt) cc_final: 0.6041 (mtp)
REVERT: C  392 LYS cc_start: 0.6876 (ttpt) cc_final: 0.6631 (tttt)
REVERT: C  417 LYS cc_start: 0.7472 (mttp) cc_final: 0.7052 (mttp)
REVERT: D  172 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6569 (mp0)
REVERT: D  258 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7778 (pt0)
  outliers start: 36
  outliers final: 20
  residues processed: 178
  average time/residue: 0.6918
  time to fit residues: 135.7450
Evaluate side-chains
  174 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  362 HIS
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  143 LYS
Chi-restraints excluded: chain B residue  153 CYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain C residue   59 ILE
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  334 GLU
Chi-restraints excluded: chain C residue  351 VAL
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  153 CYS
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain D residue  376 VAL
Chi-restraints excluded: chain D residue  394 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0060
   chunk 65 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 183 optimal weight:    0.9980
   chunk 187 optimal weight:    7.9990
   chunk 145 optimal weight:    0.0870
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.4574

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

Flipped N/Q/H residues before XYZ refinement:
A  98 ASN
C 432 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.128781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.106768 restraints weight = 24556.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.67
r_work: 0.3156 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.196  16499  Z= 0.182
  Angle     :  0.639  30.568  22243  Z= 0.286
  Chirality :  0.042   0.179   2336
  Planarity :  0.004   0.044   2858
  Dihedral  :  4.713  67.945   2530
  Min Nonbonded Distance : 1.764

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 19.67 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  1.05 (0.19), residues: 1992
  helix:  1.82 (0.17), residues: 1010
  sheet: -0.42 (0.38), residues: 174
  loop : -0.45 (0.21), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 359 
 TYR   0.011   0.001   TYR A 387 
 PHE   0.018   0.001   PHE A 409 
 TRP   0.013   0.001   TRP A 335 
 HIS   0.008   0.001   HIS B 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (16483)
  covalent geometry    : angle       0.63937 (22243)
  hydrogen bonds       : bond        0.03258 (  784)
  hydrogen bonds       : angle       4.85094 ( 2274)
  Misc. bond           : bond        0.09110 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7583 (tt0)
REVERT: A  300 PHE cc_start: 0.6811 (m-80) cc_final: 0.6480 (t80)
REVERT: A  332 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.6990 (tttm)
REVERT: A  334 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7598 (mt-10)
REVERT: A  417 LYS cc_start: 0.7379 (mttp) cc_final: 0.7052 (mttp)
REVERT: B  143 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8294 (mppt)
REVERT: B  268 GLN cc_start: 0.8113 (mt0) cc_final: 0.7841 (mt0)
REVERT: C   10 GLU cc_start: 0.6533 (mm-30) cc_final: 0.6221 (tp30)
REVERT: C  300 PHE cc_start: 0.6750 (m-80) cc_final: 0.6323 (m-80)
REVERT: C  332 LYS cc_start: 0.7788 (tttt) cc_final: 0.6989 (tttm)
REVERT: C  334 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7606 (mt-10)
REVERT: C  373 GLU cc_start: 0.7248 (mp0) cc_final: 0.7037 (pm20)
REVERT: C  391 MET cc_start: 0.6364 (mtt) cc_final: 0.6105 (mtp)
REVERT: C  392 LYS cc_start: 0.6914 (ttpt) cc_final: 0.6672 (tttt)
REVERT: C  417 LYS cc_start: 0.7462 (mttp) cc_final: 0.7081 (mttp)
REVERT: D  172 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6543 (mp0)
REVERT: D  258 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7644 (pt0)
  outliers start: 26
  outliers final: 17
  residues processed: 174
  average time/residue: 0.7261
  time to fit residues: 138.6639
Evaluate side-chains
  169 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  211 ASP
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  143 LYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  334 GLU
Chi-restraints excluded: chain C residue  351 VAL
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  153 CYS
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain D residue  376 VAL
Chi-restraints excluded: chain D residue  394 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 138 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 166 optimal weight:    4.9990
   chunk 187 optimal weight:    7.9990
   chunk 182 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 129 optimal weight:    0.9990
   chunk 154 optimal weight:    1.9990
   chunk 176 optimal weight:    1.9990
   chunk 179 optimal weight:    0.6980
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
B   4 GLN
C  98 ASN
D   4 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.126708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.104261 restraints weight = 26964.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.75
r_work: 0.3116 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.210  16499  Z= 0.198
  Angle     :  0.657  30.581  22243  Z= 0.297
  Chirality :  0.043   0.175   2336
  Planarity :  0.004   0.045   2858
  Dihedral  :  4.704  67.859   2528
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.33 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  1.00 (0.19), residues: 1992
  helix:  1.78 (0.17), residues: 1008
  sheet: -0.47 (0.37), residues: 176
  loop : -0.46 (0.21), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 359 
 TYR   0.014   0.001   TYR D  88 
 PHE   0.015   0.001   PHE A 409 
 TRP   0.013   0.001   TRP A 253 
 HIS   0.009   0.001   HIS D 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (16483)
  covalent geometry    : angle       0.65731 (22243)
  hydrogen bonds       : bond        0.03689 (  784)
  hydrogen bonds       : angle       4.90181 ( 2274)
  Misc. bond           : bond        0.09840 (   16)

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

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

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3984 Ramachandran restraints generated.
    1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A  119 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.6191 (mp10)
REVERT: A  120 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7576 (tt0)
REVERT: A  300 PHE cc_start: 0.6907 (m-80) cc_final: 0.6570 (t80)
REVERT: A  332 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7051 (tttm)
REVERT: A  334 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7620 (mt-10)
REVERT: A  417 LYS cc_start: 0.7363 (mttp) cc_final: 0.7023 (mttp)
REVERT: B  143 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8300 (mppt)
REVERT: C   10 GLU cc_start: 0.6491 (mm-30) cc_final: 0.6168 (tp30)
REVERT: C  300 PHE cc_start: 0.6798 (m-80) cc_final: 0.6438 (m-80)
REVERT: C  332 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.6997 (tttm)
REVERT: C  334 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7602 (mt-10)
REVERT: C  373 GLU cc_start: 0.7245 (mp0) cc_final: 0.7003 (pm20)
REVERT: C  391 MET cc_start: 0.6338 (mtt) cc_final: 0.6078 (mtp)
REVERT: C  392 LYS cc_start: 0.6891 (ttpt) cc_final: 0.6659 (tttt)
REVERT: C  417 LYS cc_start: 0.7411 (mttp) cc_final: 0.7015 (mttp)
REVERT: D  172 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.6609 (mp0)
  outliers start: 32
  outliers final: 19
  residues processed: 173
  average time/residue: 0.7117
  time to fit residues: 135.7882
Evaluate side-chains
  170 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   98 ASN
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue  143 LYS
Chi-restraints excluded: chain B residue  153 CYS
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  258 GLU
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  116 SER
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  332 LYS
Chi-restraints excluded: chain C residue  334 GLU
Chi-restraints excluded: chain C residue  351 VAL
Chi-restraints excluded: chain C residue  362 HIS
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  153 CYS
Chi-restraints excluded: chain D residue  172 GLU
Chi-restraints excluded: chain D residue  376 VAL
Chi-restraints excluded: chain D residue  394 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 93 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 112 optimal weight:    3.9990
   chunk 114 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0070
   chunk 40 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 189 optimal weight:    3.9990
   overall best weight:    1.1802

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

Flipped N/Q/H residues before XYZ refinement:
B   4 GLN
D   4 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.125399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.103069 restraints weight = 25887.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.71
r_work: 0.3101 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.224  16499  Z= 0.212
  Angle     :  0.672  30.599  22243  Z= 0.305
  Chirality :  0.044   0.178   2336
  Planarity :  0.004   0.045   2858
  Dihedral  :  4.743  67.665   2528
  Min Nonbonded Distance : 1.794

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 19.38 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.10 %
    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:  0.93 (0.19), residues: 1992
  helix:  1.71 (0.17), residues: 1008
  sheet: -0.47 (0.37), residues: 176
  loop : -0.49 (0.21), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  96 
 TYR   0.015   0.001   TYR D  88 
 PHE   0.018   0.001   PHE A 409 
 TRP   0.014   0.001   TRP A 253 
 HIS   0.009   0.001   HIS D 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (16483)
  covalent geometry    : angle       0.67162 (22243)
  hydrogen bonds       : bond        0.03982 (  784)
  hydrogen bonds       : angle       4.95358 ( 2274)
  Misc. bond           : bond        0.10520 (   16)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 6172.21 seconds
wall clock time: 105 minutes 46.62 seconds (6346.62 seconds total)