Starting phenix.real_space_refine
on Thu Jun 26 02:26:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d46_27176/06_2025/8d46_27176.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d46_27176/06_2025/8d46_27176.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d46_27176/06_2025/8d46_27176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d46_27176/06_2025/8d46_27176.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d46_27176/06_2025/8d46_27176.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d46_27176/06_2025/8d46_27176.cif"
  }
  resolution = 2.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.050
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: 5
    Type Number    sf(0)   Gaussians
     S      76      5.16       5
     C    9640      2.51       5
     N    2556      2.21       5
     O    2838      1.98       5
     H   15096      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 30206
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 7486
          Classifications: {'peptide': 485}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 462}
    Chain: "C"
      Number of atoms: 7616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 7616
          Classifications: {'peptide': 493}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 469}
    Chain: "D"
      Number of atoms: 7618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 7618
          Classifications: {'peptide': 493}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 469}
    Chain: "B"
      Number of atoms: 7486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 7486
          Classifications: {'peptide': 485}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 462}
  Time building chain proxies: 14.12, per 1000 atoms: 0.47
  Number of scatterers: 30206
  At special positions: 0
  Unit cell: (105.93, 112.35, 100.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      76     16.00
     O    2838      8.00
     N    2556      7.00
     C    9640      6.00
     H   15096      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 8.59
  Conformation dependent library (CDL) restraints added in 2.8 seconds
  

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3536

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 19 sheets defined
      44.4% alpha, 14.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 71
    Processing helix  chain 'A' and resid 81 through 99
    Processing helix  chain 'A' and resid 99 through 112
    Processing helix  chain 'A' and resid 114 through 121
      removed outlier: 3.610A  pdb=" N   ASN A 121 " --> pdb=" O   ASN A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 136
    Processing helix  chain 'A' and resid 171 through 187
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 199 through 213
    Processing helix  chain 'A' and resid 228 through 236
    Processing helix  chain 'A' and resid 247 through 261
    Processing helix  chain 'A' and resid 283 through 297
      removed outlier: 3.601A  pdb=" N   VAL A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 301
    Processing helix  chain 'A' and resid 312 through 330
      removed outlier: 4.469A  pdb=" N   ASP A 317 " --> pdb=" O   GLU A 313 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   GLU A 318 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 364
    Processing helix  chain 'A' and resid 394 through 399
      removed outlier: 3.525A  pdb=" N   LYS A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 422
    Processing helix  chain 'A' and resid 436 through 447
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'C' and resid 56 through 71
      removed outlier: 3.718A  pdb=" N   ALA C  66 " --> pdb=" O   LYS C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 81 through 99
    Processing helix  chain 'C' and resid 99 through 112
    Processing helix  chain 'C' and resid 114 through 121
    Processing helix  chain 'C' and resid 121 through 137
    Processing helix  chain 'C' and resid 171 through 186
      Proline residue:  C 182  - end of helix
    Processing helix  chain 'C' and resid 199 through 213
      removed outlier: 3.654A  pdb=" N   LEU C 203 " --> pdb=" O   PRO C 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 236
    Processing helix  chain 'C' and resid 247 through 261
    Processing helix  chain 'C' and resid 283 through 297
    Processing helix  chain 'C' and resid 315 through 329
      removed outlier: 3.737A  pdb=" N   GLU C 325 " --> pdb=" O   ARG C 321 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS C 329 " --> pdb=" O   GLU C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 365
    Processing helix  chain 'C' and resid 394 through 398
    Processing helix  chain 'C' and resid 413 through 423
    Processing helix  chain 'C' and resid 437 through 447
      removed outlier: 3.688A  pdb=" N   ILE C 441 " --> pdb=" O   ILE C 437 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 479 through 485
      removed outlier: 3.634A  pdb=" N   GLU C 485 " --> pdb=" O   TYR C 481 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 71
      removed outlier: 3.729A  pdb=" N   ALA D  66 " --> pdb=" O   LYS D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 80
    Processing helix  chain 'D' and resid 81 through 99
    Processing helix  chain 'D' and resid 99 through 112
    Processing helix  chain 'D' and resid 114 through 121
    Processing helix  chain 'D' and resid 121 through 137
    Processing helix  chain 'D' and resid 171 through 187
      Proline residue:  D 182  - end of helix
    Processing helix  chain 'D' and resid 199 through 213
      removed outlier: 3.654A  pdb=" N   LEU D 203 " --> pdb=" O   PRO D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 228 through 236
    Processing helix  chain 'D' and resid 247 through 261
    Processing helix  chain 'D' and resid 283 through 297
    Processing helix  chain 'D' and resid 315 through 329
      removed outlier: 3.505A  pdb=" N   LYS D 329 " --> pdb=" O   GLU D 325 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 365
    Processing helix  chain 'D' and resid 394 through 398
    Processing helix  chain 'D' and resid 413 through 422
    Processing helix  chain 'D' and resid 437 through 447
      removed outlier: 3.683A  pdb=" N   ILE D 441 " --> pdb=" O   ILE D 437 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 479 through 486
    Processing helix  chain 'B' and resid 56 through 71
    Processing helix  chain 'B' and resid 81 through 99
    Processing helix  chain 'B' and resid 99 through 112
    Processing helix  chain 'B' and resid 114 through 121
      removed outlier: 3.610A  pdb=" N   ASN B 121 " --> pdb=" O   ASN B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 136
    Processing helix  chain 'B' and resid 171 through 187
      Proline residue:  B 182  - end of helix
    Processing helix  chain 'B' and resid 199 through 213
    Processing helix  chain 'B' and resid 228 through 236
    Processing helix  chain 'B' and resid 247 through 261
    Processing helix  chain 'B' and resid 283 through 297
      removed outlier: 3.602A  pdb=" N   VAL B 295 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 301
    Processing helix  chain 'B' and resid 312 through 330
      removed outlier: 4.469A  pdb=" N   ASP B 317 " --> pdb=" O   GLU B 313 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   GLU B 318 " --> pdb=" O   SER B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 364
    Processing helix  chain 'B' and resid 394 through 399
      removed outlier: 3.524A  pdb=" N   LYS B 398 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 422
    Processing helix  chain 'B' and resid 436 through 447
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25
    Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 41
      removed outlier: 4.361A  pdb=" N   CYS A  50 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 145
      removed outlier: 4.221A  pdb=" N   THR A 153 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   VAL B 452 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   THR A 491 " --> pdb=" O   VAL B 452 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   VAL B 454 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   THR A 493 " --> pdb=" O   VAL B 454 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 219 through 221
      removed outlier: 6.216A  pdb=" N   VAL A 190 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   CYS A 163 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   LYS A 193 " --> pdb=" O   CYS A 163 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   GLN A 165 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL A 242 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   GLU A 269 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   PHE A 244 " --> pdb=" O   GLU A 269 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311
      removed outlier: 4.123A  pdb=" N   THR B 153 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 385 through 386
      removed outlier: 7.300A  pdb=" N   THR A 385 " --> pdb=" O   GLN A 406 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 23 through 25
    Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41
      removed outlier: 5.663A  pdb=" N   PHE C  38 " --> pdb=" O   GLN C  51 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   GLN C  51 " --> pdb=" O   PHE C  38 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   VAL C  40 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 145
      removed outlier: 4.325A  pdb=" N   THR C 153 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   VAL D 452 " --> pdb=" O   VAL C 489 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   THR C 491 " --> pdb=" O   VAL D 452 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   VAL D 454 " --> pdb=" O   THR C 491 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   THR C 493 " --> pdb=" O   VAL D 454 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ALA D 430 " --> pdb=" O   TRP D 453 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   SER D 274 " --> pdb=" O   ALA D 306 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   SER D 307 " --> pdb=" O   GLN D 407 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   MET D 409 " --> pdb=" O   SER D 307 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ILE D 309 " --> pdb=" O   MET D 409 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   PHE D 411 " --> pdb=" O   ILE D 309 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   VAL D 311 " --> pdb=" O   PHE D 411 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   LYS D 410 " --> pdb=" O   ASN D 389 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   VAL D 386 " --> pdb=" O   GLU D 369 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 219 through 221
      removed outlier: 6.623A  pdb=" N   CYS C 163 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   LYS C 193 " --> pdb=" O   CYS C 163 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   GLN C 165 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 367 through 368
      removed outlier: 6.654A  pdb=" N   LYS C 410 " --> pdb=" O   ASN C 389 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   SER C 307 " --> pdb=" O   GLN C 407 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   MET C 409 " --> pdb=" O   SER C 307 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ILE C 309 " --> pdb=" O   MET C 409 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   PHE C 411 " --> pdb=" O   ILE C 309 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   VAL C 311 " --> pdb=" O   PHE C 411 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   SER C 274 " --> pdb=" O   ALA C 306 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ALA C 430 " --> pdb=" O   TRP C 453 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   THR D 153 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 23 through 25
    Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 41
      removed outlier: 5.632A  pdb=" N   PHE D  38 " --> pdb=" O   GLN D  51 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   GLN D  51 " --> pdb=" O   PHE D  38 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL D  40 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 219 through 221
      removed outlier: 6.608A  pdb=" N   CYS D 163 " --> pdb=" O   VAL D 191 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   LYS D 193 " --> pdb=" O   CYS D 163 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   GLN D 165 " --> pdb=" O   LYS D 193 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 374 through 375
      removed outlier: 4.182A  pdb=" N   PHE D 381 " --> pdb=" O   TRP D 375 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 23 through 25
    Processing sheet with id=AB8, first strand: chain 'B' and resid 37 through 41
      removed outlier: 4.360A  pdb=" N   CYS B  50 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 219 through 221
      removed outlier: 6.216A  pdb=" N   VAL B 190 " --> pdb=" O   ASN B 220 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   CYS B 163 " --> pdb=" O   VAL B 191 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   LYS B 193 " --> pdb=" O   CYS B 163 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   GLN B 165 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL B 242 " --> pdb=" O   THR B 267 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   GLU B 269 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   PHE B 244 " --> pdb=" O   GLU B 269 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 385 through 386
      removed outlier: 7.300A  pdb=" N   THR B 385 " --> pdb=" O   GLN B 406 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1

    721 hydrogen bonds defined for protein.
    2094 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: 12.73

  Time building geometry restraints manager: 10.39 seconds

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

  Histogram of bond lengths:
        0.81 -     1.01: 15052
        1.01 -     1.21: 54
        1.21 -     1.41: 6269
        1.41 -     1.61: 9049
        1.61 -     1.81: 108
  Bond restraints: 30532
  Sorted by residual:
  bond pdb=" SG  CYS A 303 "
       pdb=" HG  CYS A 303 "
    ideal  model  delta    sigma   weight residual
    1.200  1.340 -0.140 2.00e-02 2.50e+03 4.87e+01
  bond pdb=" SG  CYS A 276 "
       pdb=" HG  CYS A 276 "
    ideal  model  delta    sigma   weight residual
    1.200  1.339 -0.139 2.00e-02 2.50e+03 4.85e+01
  bond pdb=" SG  CYS B 303 "
       pdb=" HG  CYS B 303 "
    ideal  model  delta    sigma   weight residual
    1.200  1.338 -0.138 2.00e-02 2.50e+03 4.79e+01
  bond pdb=" SG  CYS B 456 "
       pdb=" HG  CYS B 456 "
    ideal  model  delta    sigma   weight residual
    1.200  1.338 -0.138 2.00e-02 2.50e+03 4.74e+01
  bond pdb=" SG  CYS A 456 "
       pdb=" HG  CYS A 456 "
    ideal  model  delta    sigma   weight residual
    1.200  1.337 -0.137 2.00e-02 2.50e+03 4.71e+01
  ... (remaining 30527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 54299
        2.05 -     4.11: 923
        4.11 -     6.16: 90
        6.16 -     8.22: 13
        8.22 -    10.27: 6
  Bond angle restraints: 55331
  Sorted by residual:
  angle pdb=" N   ILE D 140 "
        pdb=" CA  ILE D 140 "
        pdb=" C   ILE D 140 "
      ideal   model   delta    sigma   weight residual
     108.89  100.23    8.66 1.32e+00 5.74e-01 4.31e+01
  angle pdb=" N   THR C 144 "
        pdb=" CA  THR C 144 "
        pdb=" C   THR C 144 "
      ideal   model   delta    sigma   weight residual
     108.73   98.46   10.27 1.63e+00 3.76e-01 3.97e+01
  angle pdb=" N   ILE C 140 "
        pdb=" CA  ILE C 140 "
        pdb=" C   ILE C 140 "
      ideal   model   delta    sigma   weight residual
     108.89  100.66    8.23 1.32e+00 5.74e-01 3.89e+01
  angle pdb=" N   THR D 144 "
        pdb=" CA  THR D 144 "
        pdb=" C   THR D 144 "
      ideal   model   delta    sigma   weight residual
     108.73   98.70   10.03 1.63e+00 3.76e-01 3.79e+01
  angle pdb=" N   LYS A 273 "
        pdb=" CA  LYS A 273 "
        pdb=" C   LYS A 273 "
      ideal   model   delta    sigma   weight residual
     108.20   99.05    9.15 1.71e+00 3.42e-01 2.86e+01
  ... (remaining 55326 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 12444
       17.94 -    35.87: 1294
       35.87 -    53.81: 437
       53.81 -    71.75: 131
       71.75 -    89.68: 27
  Dihedral angle restraints: 14333
    sinusoidal: 7821
      harmonic: 6512
  Sorted by residual:
  dihedral pdb=" CA  PRO A 168 "
           pdb=" C   PRO A 168 "
           pdb=" N   TRP A 169 "
           pdb=" CA  TRP A 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.04  -26.96     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  PRO B 168 "
           pdb=" C   PRO B 168 "
           pdb=" N   TRP B 169 "
           pdb=" CA  TRP B 169 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.09  -26.91     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" C   THR C  14 "
           pdb=" N   THR C  14 "
           pdb=" CA  THR C  14 "
           pdb=" CB  THR C  14 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.71   10.71     0      2.50e+00 1.60e-01 1.84e+01
  ... (remaining 14330 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 2014
       0.071 -    0.143: 269
       0.143 -    0.214: 13
       0.214 -    0.286: 6
       0.286 -    0.357: 2
  Chirality restraints: 2304
  Sorted by residual:
  chirality pdb=" CA  THR C  14 "
            pdb=" N   THR C  14 "
            pdb=" C   THR C  14 "
            pdb=" CB  THR C  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CA  VAL C  11 "
            pdb=" N   VAL C  11 "
            pdb=" C   VAL C  11 "
            pdb=" CB  VAL C  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.73   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CA  LYS B 273 "
            pdb=" N   LYS B 273 "
            pdb=" C   LYS B 273 "
            pdb=" CB  LYS B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.79e+00
  ... (remaining 2301 not shown)

  Planarity restraints: 4566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 121 "    0.308 2.00e-02 2.50e+03   4.13e-01 2.55e+03
        pdb=" CG  ASN D 121 "   -0.024 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 121 "   -0.308 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 121 "    0.000 2.00e-02 2.50e+03
        pdb="HD21 ASN D 121 "    0.657 2.00e-02 2.50e+03
        pdb="HD22 ASN D 121 "   -0.633 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 262 "    0.305 2.00e-02 2.50e+03   3.58e-01 1.93e+03
        pdb=" CG  ASN A 262 "   -0.016 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 262 "   -0.301 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 262 "    0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN A 262 "   -0.537 2.00e-02 2.50e+03
        pdb="HD22 ASN A 262 "    0.547 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 262 "   -0.261 2.00e-02 2.50e+03   2.82e-01 1.19e+03
        pdb=" CG  ASN B 262 "    0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 262 "    0.259 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 262 "   -0.004 2.00e-02 2.50e+03
        pdb="HD21 ASN B 262 "    0.411 2.00e-02 2.50e+03
        pdb="HD22 ASN B 262 "   -0.414 2.00e-02 2.50e+03
  ... (remaining 4563 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 1313
        2.16 -     2.77: 60542
        2.77 -     3.38: 90865
        3.38 -     3.99: 120960
        3.99 -     4.60: 190489
  Nonbonded interactions: 464169
  Sorted by model distance:
  nonbonded pdb=" HG1 THR D 442 "
            pdb=" HG  SER B 497 "
     model   vdw
     1.554 2.100
  nonbonded pdb=" O   VAL C 489 "
            pdb="HH21 ARG D 476 "
     model   vdw
     1.615 2.450
  nonbonded pdb=" H   SER C 501 "
            pdb=" O   ARG B  78 "
     model   vdw
     1.617 2.450
  nonbonded pdb=" O   ARG A  78 "
            pdb=" H   SER D 501 "
     model   vdw
     1.618 2.450
  nonbonded pdb="HH21 ARG C 476 "
            pdb=" O   VAL D 489 "
     model   vdw
     1.625 2.450
  ... (remaining 464164 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 17 through 124 or (resid 125 and (name N or name CA or nam \ 
e C or name O or name H )) or resid 126 through 501))
  selection = (chain 'B' and (resid 17 through 124 or (resid 125 and (name N or name CA or nam \ 
e C or name O or name H )) or resid 126 through 501))
  selection = (chain 'C' and ((resid 17 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ 
r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ 
Z1 or name HZ2 or name HZ3)) or resid 18 through 501))
  selection = (chain 'D' and ((resid 17 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ 
r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ 
Z1 or name HZ2 or name HZ3)) or resid 18 through 124 or (resid 125 and (name N o \ 
r name CA or name C or name O or name H )) or resid 126 through 501))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.590
  Extract box with map and model:          1.230
  Check model and map are aligned:         0.210
  Set scattering table:                    0.280
  Process input model:                     65.790
  Find NCS groups from input model:        1.090
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   84.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
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      :  0.004   0.042  15436  Z= 0.255
  Angle     :  0.772  10.272  20890  Z= 0.479
  Chirality :  0.048   0.357   2304
  Planarity :  0.005   0.092   2704
  Dihedral  : 17.106  89.682   5678
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.40 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.20), residues: 1948
  helix:  0.29 (0.18), residues: 838
  sheet: -1.30 (0.28), residues: 362
  loop : -0.96 (0.23), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 375 
 HIS   0.014   0.001   HIS C 484 
 PHE   0.011   0.001   PHE D 483 
 TYR   0.018   0.002   TYR D 351 
 ARG   0.008   0.001   ARG B 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15331 (  721)
  hydrogen bonds       : angle       7.20812 ( 2094)
  covalent geometry    : bond        0.00421 (15436)
  covalent geometry    : angle       0.77249 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 198
  time to evaluate  : 4.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LYS cc_start: 0.5511 (mmpt) cc_final: 0.5266 (mmpt)
REVERT: C   46 GLU cc_start: 0.7724 (mp0) cc_final: 0.7213 (mp0)
REVERT: D  348 LYS cc_start: 0.8274 (mttt) cc_final: 0.7602 (mmtt)
REVERT: B   65 LYS cc_start: 0.5489 (mmpt) cc_final: 0.5245 (mmpt)
  outliers start: 48
  outliers final: 33
  residues processed: 239
  average time/residue: 2.1345
  time to fit residues: 586.2121
Evaluate side-chains
  208 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 175
  time to evaluate  : 2.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain C residue   34 SER
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  256 GLU
Chi-restraints excluded: chain C residue  311 VAL
Chi-restraints excluded: chain C residue  370 CYS
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  464 CYS
Chi-restraints excluded: chain C residue  497 SER
Chi-restraints excluded: chain D residue  209 ILE
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  247 SER
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  497 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  497 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 163 optimal weight:    4.9990
   chunk 147 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 99 optimal weight:    0.5980
   chunk 78 optimal weight:    0.6980
   chunk 152 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 113 optimal weight:    0.5980
   chunk 176 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 292 HIS
A 293 HIS
D 117 ASN
D 121 ASN
D 389 ASN
D 474 ASN
** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.183850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.142351 restraints weight = 45144.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.77
r_work: 0.3582 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.0781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15436  Z= 0.136
  Angle     :  0.541   5.454  20890  Z= 0.292
  Chirality :  0.043   0.139   2304
  Planarity :  0.005   0.085   2704
  Dihedral  :  6.814  80.983   2139
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.54 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 23.51 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.20), residues: 1948
  helix:  0.82 (0.18), residues: 842
  sheet: -1.30 (0.26), residues: 382
  loop : -0.99 (0.24), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 375 
 HIS   0.011   0.002   HIS C 484 
 PHE   0.016   0.001   PHE D 483 
 TYR   0.012   0.001   TYR C 316 
 ARG   0.003   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04655 (  721)
  hydrogen bonds       : angle       5.38665 ( 2094)
  covalent geometry    : bond        0.00294 (15436)
  covalent geometry    : angle       0.54124 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 188
  time to evaluate  : 2.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.5695 (mm-30) cc_final: 0.5301 (mm-30)
REVERT: A  436 ASP cc_start: 0.7103 (t70) cc_final: 0.6598 (t70)
REVERT: C   52 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8470 (t)
REVERT: D   46 GLU cc_start: 0.7947 (mp0) cc_final: 0.7652 (mp0)
REVERT: D  256 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6653 (tp30)
REVERT: B   46 GLU cc_start: 0.5676 (mm-30) cc_final: 0.5284 (mm-30)
REVERT: B   61 ASP cc_start: 0.4760 (t70) cc_final: 0.4532 (m-30)
REVERT: B  436 ASP cc_start: 0.7213 (t70) cc_final: 0.6672 (t70)
  outliers start: 47
  outliers final: 29
  residues processed: 221
  average time/residue: 2.1955
  time to fit residues: 557.0877
Evaluate side-chains
  205 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 174
  time to evaluate  : 2.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   19 GLN
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  330 TYR
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  370 CYS
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain D residue  209 ILE
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  484 HIS
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  497 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 143 optimal weight:    3.9990
   chunk 164 optimal weight:    7.9990
   chunk 154 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0000
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 179 optimal weight:    0.6980
   chunk 148 optimal weight:    0.1980
   overall best weight:    0.7786

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

Flipped N/Q/H residues before XYZ refinement:
D 117 ASN
D 474 ASN
B 292 HIS
B 293 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.183920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.142282 restraints weight = 45447.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 1.79
r_work: 0.3573 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  15436  Z= 0.127
  Angle     :  0.512   5.067  20890  Z= 0.275
  Chirality :  0.042   0.150   2304
  Planarity :  0.005   0.081   2704
  Dihedral  :  6.032  69.836   2122
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 23.39 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.19), residues: 1948
  helix:  0.99 (0.18), residues: 842
  sheet: -1.34 (0.26), residues: 382
  loop : -1.02 (0.23), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.010   0.001   HIS C 484 
 PHE   0.014   0.001   PHE A  38 
 TYR   0.010   0.001   TYR C 316 
 ARG   0.002   0.000   ARG C 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04032 (  721)
  hydrogen bonds       : angle       5.05710 ( 2094)
  covalent geometry    : bond        0.00290 (15436)
  covalent geometry    : angle       0.51170 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 186
  time to evaluate  : 2.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.4701 (t70) cc_final: 0.4491 (m-30)
REVERT: A  436 ASP cc_start: 0.7020 (t70) cc_final: 0.6606 (t70)
REVERT: D  143 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7634 (mtp85)
REVERT: D  256 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6790 (tp30)
REVERT: D  484 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.6517 (p-80)
REVERT: D  485 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6641 (mm-30)
REVERT: B   46 GLU cc_start: 0.5786 (mm-30) cc_final: 0.5349 (mm-30)
REVERT: B  436 ASP cc_start: 0.7066 (t70) cc_final: 0.6614 (t70)
  outliers start: 40
  outliers final: 29
  residues processed: 214
  average time/residue: 2.1207
  time to fit residues: 522.3697
Evaluate side-chains
  209 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 3.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   19 GLN
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  247 SER
Chi-restraints excluded: chain C residue  330 TYR
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain D residue  209 ILE
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  348 LYS
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  484 HIS
Chi-restraints excluded: chain D residue  491 THR
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 160 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 158 optimal weight:    0.6980
   chunk 143 optimal weight:    2.9990
   chunk 103 optimal weight:    0.1980
   chunk 13 optimal weight:    0.1980
   chunk 183 optimal weight:    4.9990
   chunk 119 optimal weight:    1.9990
   chunk 185 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
D 117 ASN
D 474 ASN
B  42 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.184172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.142636 restraints weight = 45315.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 1.78
r_work: 0.3560 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15436  Z= 0.126
  Angle     :  0.503   6.000  20890  Z= 0.269
  Chirality :  0.042   0.135   2304
  Planarity :  0.005   0.079   2704
  Dihedral  :  5.870  67.938   2119
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.95 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 22.83 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.19), residues: 1948
  helix:  1.09 (0.18), residues: 842
  sheet: -1.27 (0.26), residues: 372
  loop : -1.02 (0.23), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 375 
 HIS   0.009   0.001   HIS C 484 
 PHE   0.016   0.001   PHE A  38 
 TYR   0.009   0.001   TYR C 316 
 ARG   0.003   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  721)
  hydrogen bonds       : angle       4.86547 ( 2094)
  covalent geometry    : bond        0.00287 (15436)
  covalent geometry    : angle       0.50321 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 189
  time to evaluate  : 2.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.4705 (t70) cc_final: 0.4497 (m-30)
REVERT: A  106 MET cc_start: 0.6102 (tmm) cc_final: 0.5806 (tmm)
REVERT: A  368 LEU cc_start: 0.7577 (tt) cc_final: 0.6730 (mm)
REVERT: A  436 ASP cc_start: 0.7009 (t70) cc_final: 0.6609 (t70)
REVERT: C   52 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8458 (t)
REVERT: C  262 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7629 (p0)
REVERT: D  143 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7672 (mtp85)
REVERT: D  256 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6846 (tp30)
REVERT: D  320 VAL cc_start: 0.8550 (t) cc_final: 0.8288 (p)
REVERT: D  484 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6972 (p-80)
REVERT: B  106 MET cc_start: 0.6144 (tmm) cc_final: 0.5843 (tmm)
REVERT: B  436 ASP cc_start: 0.7026 (t70) cc_final: 0.6614 (t70)
  outliers start: 44
  outliers final: 29
  residues processed: 223
  average time/residue: 2.0939
  time to fit residues: 536.6618
Evaluate side-chains
  215 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 182
  time to evaluate  : 2.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASN
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain C residue   19 GLN
Chi-restraints excluded: chain C residue   27 ASN
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  256 GLU
Chi-restraints excluded: chain C residue  262 ASN
Chi-restraints excluded: chain C residue  330 TYR
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  348 LYS
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  388 SER
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  484 HIS
Chi-restraints excluded: chain D residue  491 THR
Chi-restraints excluded: chain B residue   42 ASN
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 183 optimal weight:    7.9990
   chunk 171 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 165 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 166 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 116 optimal weight:    0.0870
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
C 220 ASN
D 117 ASN
D 474 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.184194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.143051 restraints weight = 45273.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.77
r_work: 0.3585 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15436  Z= 0.123
  Angle     :  0.500   5.330  20890  Z= 0.268
  Chirality :  0.042   0.141   2304
  Planarity :  0.005   0.083   2704
  Dihedral  :  5.713  67.092   2115
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.95 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 23.21 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.20), residues: 1948
  helix:  1.19 (0.18), residues: 842
  sheet: -1.26 (0.26), residues: 372
  loop : -0.98 (0.23), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 375 
 HIS   0.008   0.001   HIS C 484 
 PHE   0.014   0.001   PHE A  38 
 TYR   0.008   0.001   TYR D 316 
 ARG   0.003   0.000   ARG C 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  721)
  hydrogen bonds       : angle       4.79911 ( 2094)
  covalent geometry    : bond        0.00283 (15436)
  covalent geometry    : angle       0.49964 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 190
  time to evaluate  : 3.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  436 ASP cc_start: 0.6974 (t70) cc_final: 0.6606 (t70)
REVERT: C   16 LEU cc_start: 0.6017 (mt) cc_final: 0.5708 (mm)
REVERT: C   52 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8452 (t)
REVERT: C  262 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7633 (p0)
REVERT: D  256 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6782 (tp30)
REVERT: D  320 VAL cc_start: 0.8554 (t) cc_final: 0.8212 (p)
REVERT: D  484 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6995 (p-80)
REVERT: D  485 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7137 (mm-30)
REVERT: B  436 ASP cc_start: 0.7074 (t70) cc_final: 0.6697 (t70)
  outliers start: 41
  outliers final: 27
  residues processed: 220
  average time/residue: 2.6093
  time to fit residues: 666.7322
Evaluate side-chains
  210 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 179
  time to evaluate  : 3.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain C residue   19 GLN
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  247 SER
Chi-restraints excluded: chain C residue  262 ASN
Chi-restraints excluded: chain C residue  330 TYR
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain D residue  209 ILE
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  348 LYS
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  388 SER
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  484 HIS
Chi-restraints excluded: chain D residue  491 THR
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 136 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 113 optimal weight:    0.1980
   chunk 164 optimal weight:    0.5980
   chunk 92 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9990
   chunk 161 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 ASN
D 117 ASN
D 220 ASN
D 474 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.184339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.142195 restraints weight = 45193.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 1.85
r_work: 0.3556 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15436  Z= 0.132
  Angle     :  0.505   5.046  20890  Z= 0.269
  Chirality :  0.042   0.136   2304
  Planarity :  0.005   0.082   2704
  Dihedral  :  5.708  66.063   2115
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.90 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.08 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.19), residues: 1948
  helix:  1.22 (0.18), residues: 838
  sheet: -1.30 (0.26), residues: 378
  loop : -1.01 (0.23), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 375 
 HIS   0.008   0.001   HIS C 484 
 PHE   0.022   0.001   PHE A  24 
 TYR   0.010   0.001   TYR D 316 
 ARG   0.004   0.000   ARG A 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03677 (  721)
  hydrogen bonds       : angle       4.75583 ( 2094)
  covalent geometry    : bond        0.00305 (15436)
  covalent geometry    : angle       0.50502 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 185
  time to evaluate  : 6.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 MET cc_start: 0.6151 (tmm) cc_final: 0.5917 (tmm)
REVERT: A  368 LEU cc_start: 0.7574 (tt) cc_final: 0.6734 (mm)
REVERT: A  436 ASP cc_start: 0.7045 (t70) cc_final: 0.6674 (t70)
REVERT: C  262 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7570 (p0)
REVERT: D   56 ASP cc_start: 0.7775 (t0) cc_final: 0.7520 (t70)
REVERT: D  320 VAL cc_start: 0.8549 (t) cc_final: 0.8223 (p)
REVERT: D  484 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.7096 (p-80)
REVERT: B  106 MET cc_start: 0.6193 (tmm) cc_final: 0.5959 (tmm)
REVERT: B  436 ASP cc_start: 0.7132 (t70) cc_final: 0.6755 (t70)
  outliers start: 43
  outliers final: 37
  residues processed: 216
  average time/residue: 2.8565
  time to fit residues: 730.4348
Evaluate side-chains
  219 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 180
  time to evaluate  : 5.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   19 GLN
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  247 SER
Chi-restraints excluded: chain C residue  256 GLU
Chi-restraints excluded: chain C residue  262 ASN
Chi-restraints excluded: chain C residue  330 TYR
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain C residue  497 SER
Chi-restraints excluded: chain D residue  209 ILE
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  348 LYS
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  388 SER
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  484 HIS
Chi-restraints excluded: chain D residue  491 THR
Chi-restraints excluded: chain D residue  497 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 114 optimal weight:    0.9980
   chunk 132 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 153 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 165 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  19 GLN
C 220 ASN
D 117 ASN
D 474 ASN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.179718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.137537 restraints weight = 45533.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 1.82
r_work: 0.3523 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  15436  Z= 0.249
  Angle     :  0.588   5.897  20890  Z= 0.320
  Chirality :  0.045   0.138   2304
  Planarity :  0.006   0.084   2704
  Dihedral  :  6.057  65.028   2115
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.62 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 23.27 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.19), residues: 1948
  helix:  0.64 (0.18), residues: 844
  sheet: -1.51 (0.26), residues: 372
  loop : -1.16 (0.23), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 375 
 HIS   0.014   0.002   HIS C 484 
 PHE   0.022   0.002   PHE A  24 
 TYR   0.014   0.002   TYR D 426 
 ARG   0.006   0.001   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04575 (  721)
  hydrogen bonds       : angle       5.00898 ( 2094)
  covalent geometry    : bond        0.00583 (15436)
  covalent geometry    : angle       0.58761 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 179
  time to evaluate  : 2.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.5425 (mm-30) cc_final: 0.5051 (mm-30)
REVERT: A  106 MET cc_start: 0.6294 (tmm) cc_final: 0.5924 (tmm)
REVERT: D   46 GLU cc_start: 0.7842 (mp0) cc_final: 0.7158 (mp0)
REVERT: D  320 VAL cc_start: 0.8604 (t) cc_final: 0.8360 (p)
REVERT: D  484 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.7246 (p-80)
REVERT: B   90 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7565 (m-80)
REVERT: B  106 MET cc_start: 0.6329 (tmm) cc_final: 0.5955 (tmm)
  outliers start: 49
  outliers final: 38
  residues processed: 210
  average time/residue: 2.6263
  time to fit residues: 639.6559
Evaluate side-chains
  215 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 175
  time to evaluate  : 2.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  247 SER
Chi-restraints excluded: chain C residue  256 GLU
Chi-restraints excluded: chain C residue  330 TYR
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain C residue  497 SER
Chi-restraints excluded: chain D residue  209 ILE
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  348 LYS
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  388 SER
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  484 HIS
Chi-restraints excluded: chain D residue  491 THR
Chi-restraints excluded: chain D residue  497 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  391 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 137 optimal weight:    1.9990
   chunk 138 optimal weight:    0.9980
   chunk 129 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 174 optimal weight:    4.9990
   chunk 164 optimal weight:    5.9990
   chunk 107 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  19 GLN
D 117 ASN
D 220 ASN
D 474 ASN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.182962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.141701 restraints weight = 45542.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.78
r_work: 0.3566 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15436  Z= 0.125
  Angle     :  0.520   7.362  20890  Z= 0.277
  Chirality :  0.042   0.136   2304
  Planarity :  0.005   0.079   2704
  Dihedral  :  5.865  66.898   2115
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 23.58 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.19), residues: 1948
  helix:  1.03 (0.18), residues: 838
  sheet: -1.50 (0.25), residues: 378
  loop : -1.08 (0.23), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 375 
 HIS   0.008   0.001   HIS D 484 
 PHE   0.026   0.001   PHE A  24 
 TYR   0.011   0.001   TYR D 316 
 ARG   0.007   0.000   ARG B 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  721)
  hydrogen bonds       : angle       4.78592 ( 2094)
  covalent geometry    : bond        0.00285 (15436)
  covalent geometry    : angle       0.52014 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 181
  time to evaluate  : 2.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.5660 (mm-30) cc_final: 0.5276 (mm-30)
REVERT: A  106 MET cc_start: 0.6167 (tmm) cc_final: 0.5821 (tmm)
REVERT: A  368 LEU cc_start: 0.7591 (tt) cc_final: 0.6729 (mm)
REVERT: A  436 ASP cc_start: 0.7224 (t70) cc_final: 0.6765 (t70)
REVERT: D   46 GLU cc_start: 0.7756 (mp0) cc_final: 0.7041 (mp0)
REVERT: D  320 VAL cc_start: 0.8558 (t) cc_final: 0.8341 (p)
REVERT: B   46 GLU cc_start: 0.5637 (mm-30) cc_final: 0.5419 (mm-30)
REVERT: B   90 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7620 (m-80)
REVERT: B  106 MET cc_start: 0.6170 (tmm) cc_final: 0.5819 (tmm)
REVERT: B  436 ASP cc_start: 0.7285 (t70) cc_final: 0.6801 (t70)
  outliers start: 42
  outliers final: 35
  residues processed: 211
  average time/residue: 2.2361
  time to fit residues: 541.3139
Evaluate side-chains
  210 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 174
  time to evaluate  : 2.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain C residue   13 LEU
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  247 SER
Chi-restraints excluded: chain C residue  330 TYR
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain C residue  497 SER
Chi-restraints excluded: chain D residue  209 ILE
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  311 VAL
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  348 LYS
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  491 THR
Chi-restraints excluded: chain D residue  497 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 159 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 181 optimal weight:    9.9990
   chunk 143 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 182 optimal weight:    1.9990
   chunk 172 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  19 GLN
D 474 ASN
D 498 GLN
B  42 ASN
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.181606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.139056 restraints weight = 45409.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.84
r_work: 0.3526 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  15436  Z= 0.198
  Angle     :  0.555   5.429  20890  Z= 0.299
  Chirality :  0.044   0.144   2304
  Planarity :  0.005   0.088   2704
  Dihedral  :  5.962  65.565   2115
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.41 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 23.51 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.19), residues: 1948
  helix:  0.84 (0.18), residues: 840
  sheet: -1.59 (0.25), residues: 378
  loop : -1.11 (0.23), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 375 
 HIS   0.011   0.002   HIS C 484 
 PHE   0.034   0.002   PHE A  24 
 TYR   0.012   0.002   TYR D 351 
 ARG   0.007   0.001   ARG C 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04169 (  721)
  hydrogen bonds       : angle       4.88490 ( 2094)
  covalent geometry    : bond        0.00463 (15436)
  covalent geometry    : angle       0.55545 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 175
  time to evaluate  : 2.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.5709 (mm-30) cc_final: 0.5325 (mm-30)
REVERT: A   91 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.6803 (ttmt)
REVERT: D  284 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7007 (tp)
REVERT: D  320 VAL cc_start: 0.8619 (t) cc_final: 0.8391 (p)
REVERT: B   46 GLU cc_start: 0.5720 (mm-30) cc_final: 0.5510 (mm-30)
REVERT: B   90 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7639 (m-80)
REVERT: B   91 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.6798 (ttmt)
REVERT: B  106 MET cc_start: 0.6231 (tmm) cc_final: 0.5971 (tmm)
  outliers start: 46
  outliers final: 37
  residues processed: 208
  average time/residue: 2.2493
  time to fit residues: 534.4181
Evaluate side-chains
  212 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 171
  time to evaluate  : 2.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  247 SER
Chi-restraints excluded: chain C residue  256 GLU
Chi-restraints excluded: chain C residue  330 TYR
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain C residue  491 THR
Chi-restraints excluded: chain C residue  497 SER
Chi-restraints excluded: chain D residue  209 ILE
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  348 LYS
Chi-restraints excluded: chain D residue  388 SER
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  491 THR
Chi-restraints excluded: chain D residue  497 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 185 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 131 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 170 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 141 optimal weight:    1.9990
   chunk 146 optimal weight:    8.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  19 GLN
D 474 ASN
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.182260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.139822 restraints weight = 45429.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 1.84
r_work: 0.3538 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15436  Z= 0.165
  Angle     :  0.540   5.207  20890  Z= 0.291
  Chirality :  0.043   0.144   2304
  Planarity :  0.005   0.082   2704
  Dihedral  :  5.942  66.087   2115
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.16 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 23.82 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.19), residues: 1948
  helix:  0.89 (0.18), residues: 840
  sheet: -1.58 (0.25), residues: 378
  loop : -1.09 (0.23), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 375 
 HIS   0.009   0.002   HIS D 484 
 PHE   0.016   0.001   PHE D 483 
 TYR   0.011   0.002   TYR D  90 
 ARG   0.003   0.000   ARG A 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03973 (  721)
  hydrogen bonds       : angle       4.83155 ( 2094)
  covalent geometry    : bond        0.00381 (15436)
  covalent geometry    : angle       0.54022 (20890)

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

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

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3896 Ramachandran restraints generated.
    1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 174
  time to evaluate  : 2.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.5625 (mm-30) cc_final: 0.5422 (mm-30)
REVERT: A   91 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.6831 (ttmt)
REVERT: A  368 LEU cc_start: 0.7658 (tt) cc_final: 0.6762 (mm)
REVERT: A  436 ASP cc_start: 0.7341 (t70) cc_final: 0.6888 (t70)
REVERT: D  284 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7002 (tp)
REVERT: D  320 VAL cc_start: 0.8613 (t) cc_final: 0.8391 (p)
REVERT: B   46 GLU cc_start: 0.5681 (mm-30) cc_final: 0.5464 (mm-30)
REVERT: B   90 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7616 (m-80)
REVERT: B   91 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.6817 (ttmt)
REVERT: B  106 MET cc_start: 0.6229 (tmm) cc_final: 0.5966 (tmm)
REVERT: B  436 ASP cc_start: 0.7360 (t70) cc_final: 0.6884 (t70)
  outliers start: 43
  outliers final: 34
  residues processed: 208
  average time/residue: 2.2168
  time to fit residues: 525.1648
Evaluate side-chains
  211 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 173
  time to evaluate  : 2.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue   91 LYS
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  209 ILE
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  247 SER
Chi-restraints excluded: chain C residue  330 TYR
Chi-restraints excluded: chain C residue  349 GLU
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  402 PHE
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain C residue  442 THR
Chi-restraints excluded: chain C residue  497 SER
Chi-restraints excluded: chain D residue  209 ILE
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  256 GLU
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  330 TYR
Chi-restraints excluded: chain D residue  348 LYS
Chi-restraints excluded: chain D residue  349 GLU
Chi-restraints excluded: chain D residue  388 SER
Chi-restraints excluded: chain D residue  402 PHE
Chi-restraints excluded: chain D residue  417 VAL
Chi-restraints excluded: chain D residue  442 THR
Chi-restraints excluded: chain D residue  491 THR
Chi-restraints excluded: chain D residue  497 SER
Chi-restraints excluded: chain B residue   56 ASP
Chi-restraints excluded: chain B residue   87 ARG
Chi-restraints excluded: chain B residue   90 TYR
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  266 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 194
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 188 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 130 optimal weight:    0.9990
   chunk 159 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 1 optimal weight:    7.9990
   chunk 192 optimal weight:    6.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  19 GLN
D 474 ASN
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.181116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.138624 restraints weight = 45430.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 1.84
r_work: 0.3500 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  15436  Z= 0.208
  Angle     :  0.566   5.460  20890  Z= 0.307
  Chirality :  0.044   0.143   2304
  Planarity :  0.005   0.089   2704
  Dihedral  :  6.010  65.562   2111
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.57 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 24.07 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.19), residues: 1948
  helix:  0.72 (0.18), residues: 840
  sheet: -1.63 (0.25), residues: 370
  loop : -1.12 (0.23), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 375 
 HIS   0.011   0.002   HIS C 484 
 PHE   0.013   0.002   PHE B  24 
 TYR   0.017   0.002   TYR C 351 
 ARG   0.004   0.001   ARG C 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04267 (  721)
  hydrogen bonds       : angle       4.91855 ( 2094)
  covalent geometry    : bond        0.00489 (15436)
  covalent geometry    : angle       0.56645 (20890)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 20795.38 seconds
wall clock time: 365 minutes 56.85 seconds (21956.85 seconds total)