Starting phenix.real_space_refine
on Sat Aug 23 03:06:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ca1_16515/08_2025/8ca1_16515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ca1_16515/08_2025/8ca1_16515.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ca1_16515/08_2025/8ca1_16515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ca1_16515/08_2025/8ca1_16515.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ca1_16515/08_2025/8ca1_16515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ca1_16515/08_2025/8ca1_16515.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.254
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
     P       4      5.49       5
     S      50      5.16       5
     C    5708      2.51       5
     N    1566      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9036
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4465
          Classifications: {'peptide': 589}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570}
    Chain: "A"
      Number of atoms: 4465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4465
          Classifications: {'peptide': 589}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 570}
    Chain: "B"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.98, per 1000 atoms: 0.22
  Number of scatterers: 9036
  At special positions: 0
  Unit cell: (85.176, 112.216, 86.528, 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      50     16.00
     P       4     15.00
     O    1708      8.00
     N    1566      7.00
     C    5708      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 408.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 6 sheets defined
      67.1% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'B' and resid 73 through 80
    Processing helix  chain 'B' and resid 84 through 88
      removed outlier: 3.965A  pdb=" N   GLN B  87 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 117
      removed outlier: 4.036A  pdb=" N   GLY B 108 " --> pdb=" O   LYS B 104 " (cutoff:3.500A)
      Proline residue:  B 109  - end of helix
    Processing helix  chain 'B' and resid 119 through 127
    Processing helix  chain 'B' and resid 130 through 140
      removed outlier: 3.878A  pdb=" N   GLY B 136 " --> pdb=" O   ASP B 132 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU B 137 " --> pdb=" O   THR B 133 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU B 139 " --> pdb=" O   GLN B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 145
      removed outlier: 4.130A  pdb=" N   LEU B 145 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 152
    Processing helix  chain 'B' and resid 157 through 170
    Processing helix  chain 'B' and resid 172 through 185
      removed outlier: 3.934A  pdb=" N   ILE B 185 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 193
      removed outlier: 3.743A  pdb=" N   LEU B 191 " --> pdb=" O   PHE B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 208
      Proline residue:  B 204  - end of helix
      removed outlier: 3.766A  pdb=" N   SER B 208 " --> pdb=" O   PRO B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
    Processing helix  chain 'B' and resid 288 through 290
      No H-bonds generated for 'chain 'B' and resid 288 through 290'
    Processing helix  chain 'B' and resid 329 through 367
      removed outlier: 4.677A  pdb=" N   PHE B 343 " --> pdb=" O   ASN B 339 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   GLY B 344 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   MET B 345 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA B 346 " --> pdb=" O   ARG B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 408
      removed outlier: 3.754A  pdb=" N   MET B 400 " --> pdb=" O   SER B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 444
      removed outlier: 3.681A  pdb=" N   TRP B 428 " --> pdb=" O   SER B 424 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   GLY B 440 " --> pdb=" O   GLN B 436 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   MET B 441 " --> pdb=" O   ILE B 437 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   MET B 444 " --> pdb=" O   GLY B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 457
    Processing helix  chain 'B' and resid 458 through 461
    Processing helix  chain 'B' and resid 465 through 493
      removed outlier: 4.856A  pdb=" N   ASP B 480 " --> pdb=" O   GLN B 476 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   LYS B 481 " --> pdb=" O   GLY B 477 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLY B 482 " --> pdb=" O   CYS B 478 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY B 489 " --> pdb=" O   LEU B 485 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS B 493 " --> pdb=" O   GLY B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 513
    Processing helix  chain 'B' and resid 527 through 529
      No H-bonds generated for 'chain 'B' and resid 527 through 529'
    Processing helix  chain 'B' and resid 530 through 556
      removed outlier: 3.598A  pdb=" N   ALA B 537 " --> pdb=" O   SER B 533 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B 538 " --> pdb=" O   GLY B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 561
      removed outlier: 3.771A  pdb=" N   VAL B 560 " --> pdb=" O   LYS B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 593
      removed outlier: 3.505A  pdb=" N   ARG B 568 " --> pdb=" O   PHE B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 624
      removed outlier: 3.690A  pdb=" N   SER B 624 " --> pdb=" O   ALA B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 646
    Processing helix  chain 'A' and resid 73 through 80
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.972A  pdb=" N   GLN A  87 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 117
      removed outlier: 4.027A  pdb=" N   GLY A 108 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
      Proline residue:  A 109  - end of helix
    Processing helix  chain 'A' and resid 119 through 127
    Processing helix  chain 'A' and resid 130 through 140
      removed outlier: 3.880A  pdb=" N   GLY A 136 " --> pdb=" O   ASP A 132 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A 137 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU A 139 " --> pdb=" O   GLN A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 145
      removed outlier: 4.126A  pdb=" N   LEU A 145 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 157 through 170
    Processing helix  chain 'A' and resid 172 through 185
      removed outlier: 3.933A  pdb=" N   ILE A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 193
      removed outlier: 3.743A  pdb=" N   LEU A 191 " --> pdb=" O   PHE A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 208
      Proline residue:  A 204  - end of helix
      removed outlier: 3.766A  pdb=" N   SER A 208 " --> pdb=" O   PRO A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 229
    Processing helix  chain 'A' and resid 288 through 290
      No H-bonds generated for 'chain 'A' and resid 288 through 290'
    Processing helix  chain 'A' and resid 329 through 367
      removed outlier: 4.677A  pdb=" N   PHE A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   GLY A 344 " --> pdb=" O   ASN A 340 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   MET A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A 346 " --> pdb=" O   ARG A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 408
      removed outlier: 3.739A  pdb=" N   MET A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 444
      removed outlier: 3.685A  pdb=" N   TRP A 428 " --> pdb=" O   SER A 424 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   GLY A 440 " --> pdb=" O   GLN A 436 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   MET A 441 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   MET A 444 " --> pdb=" O   GLY A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 457
    Processing helix  chain 'A' and resid 458 through 461
    Processing helix  chain 'A' and resid 465 through 493
      removed outlier: 4.881A  pdb=" N   ASP A 480 " --> pdb=" O   GLN A 476 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LYS A 481 " --> pdb=" O   GLY A 477 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLY A 482 " --> pdb=" O   CYS A 478 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS A 493 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 513
    Processing helix  chain 'A' and resid 527 through 529
      No H-bonds generated for 'chain 'A' and resid 527 through 529'
    Processing helix  chain 'A' and resid 530 through 556
      removed outlier: 3.507A  pdb=" N   LEU A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA A 537 " --> pdb=" O   SER A 533 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 561
      removed outlier: 3.776A  pdb=" N   VAL A 560 " --> pdb=" O   LYS A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 593
      removed outlier: 3.506A  pdb=" N   ARG A 568 " --> pdb=" O   PHE A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 624
      removed outlier: 3.687A  pdb=" N   SER A 624 " --> pdb=" O   ALA A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 646
    Processing sheet with id=AA1, first strand: chain 'B' and resid 213 through 216
      removed outlier: 5.718A  pdb=" N   ALA B 214 " --> pdb=" O   THR B 261 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   PHE B 263 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   CYS B 216 " --> pdb=" O   PHE B 263 " (cutoff:3.500A)
      removed outlier: 9.259A  pdb=" N   LYS B 265 " --> pdb=" O   CYS B 216 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   ALA B 282 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 235
      removed outlier: 6.208A  pdb=" N   TYR B 241 " --> pdb=" O   PRO B 319 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   THR B 243 " --> pdb=" O   LYS B 317 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   LYS B 317 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ASN B 245 " --> pdb=" O   GLY B 315 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   GLY B 315 " --> pdb=" O   ASN B 245 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER B 247 " --> pdb=" O   PHE B 313 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   PHE B 313 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   ILE B 249 " --> pdb=" O   VAL B 311 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 311 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 369
    Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 216
      removed outlier: 5.722A  pdb=" N   ALA A 214 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   PHE A 263 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   CYS A 216 " --> pdb=" O   PHE A 263 " (cutoff:3.500A)
      removed outlier: 9.244A  pdb=" N   LYS A 265 " --> pdb=" O   CYS A 216 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   ALA A 282 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 235
      removed outlier: 6.210A  pdb=" N   TYR A 241 " --> pdb=" O   PRO A 319 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   THR A 243 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LYS A 317 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ASN A 245 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   GLY A 315 " --> pdb=" O   ASN A 245 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER A 247 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   PHE A 313 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
      removed outlier: 5.359A  pdb=" N   ILE A 249 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   VAL A 311 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 368 through 369

    569 hydrogen bonds defined for protein.
    1647 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3002
        1.34 -     1.46: 1931
        1.46 -     1.58: 4172
        1.58 -     1.70: 1
        1.70 -     1.82: 86
  Bond restraints: 9192
  Sorted by residual:
  bond pdb=" O5B FAD B 701 "
       pdb=" PA  FAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.634  1.528  0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" O3P FAD B 701 "
       pdb=" P   FAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.660  1.557  0.103 2.00e-02 2.50e+03 2.63e+01
  bond pdb=" O3P FAD A 701 "
       pdb=" P   FAD A 701 "
    ideal  model  delta    sigma   weight residual
    1.660  1.566  0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" O5B FAD A 701 "
       pdb=" PA  FAD A 701 "
    ideal  model  delta    sigma   weight residual
    1.634  1.541  0.093 2.00e-02 2.50e+03 2.18e+01
  bond pdb=" O5' FAD B 701 "
       pdb=" P   FAD B 701 "
    ideal  model  delta    sigma   weight residual
    1.637  1.570  0.067 2.00e-02 2.50e+03 1.12e+01
  ... (remaining 9187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 12176
        2.75 -     5.51: 210
        5.51 -     8.26: 10
        8.26 -    11.02: 3
       11.02 -    13.77: 1
  Bond angle restraints: 12400
  Sorted by residual:
  angle pdb=" CB  MET B 301 "
        pdb=" CG  MET B 301 "
        pdb=" SD  MET B 301 "
      ideal   model   delta    sigma   weight residual
     112.70  126.47  -13.77 3.00e+00 1.11e-01 2.11e+01
  angle pdb=" N   GLU B 450 "
        pdb=" CA  GLU B 450 "
        pdb=" CB  GLU B 450 "
      ideal   model   delta    sigma   weight residual
     110.12  104.63    5.49 1.47e+00 4.63e-01 1.39e+01
  angle pdb=" N   GLU A 450 "
        pdb=" CA  GLU A 450 "
        pdb=" CB  GLU A 450 "
      ideal   model   delta    sigma   weight residual
     110.12  104.94    5.18 1.47e+00 4.63e-01 1.24e+01
  angle pdb=" C   MET A 301 "
        pdb=" CA  MET A 301 "
        pdb=" CB  MET A 301 "
      ideal   model   delta    sigma   weight residual
     110.32  103.14    7.18 2.11e+00 2.25e-01 1.16e+01
  angle pdb=" CA  GLU A 450 "
        pdb=" CB  GLU A 450 "
        pdb=" CG  GLU A 450 "
      ideal   model   delta    sigma   weight residual
     114.10  120.60   -6.50 2.00e+00 2.50e-01 1.06e+01
  ... (remaining 12395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.11: 5199
       22.11 -    44.21: 310
       44.21 -    66.32: 38
       66.32 -    88.43: 15
       88.43 -   110.53: 4
  Dihedral angle restraints: 5566
    sinusoidal: 2256
      harmonic: 3310
  Sorted by residual:
  dihedral pdb=" CA  LYS B 493 "
           pdb=" C   LYS B 493 "
           pdb=" N   ASN B 494 "
           pdb=" CA  ASN B 494 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.20   27.80     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  LYS A 493 "
           pdb=" C   LYS A 493 "
           pdb=" N   ASN A 494 "
           pdb=" CA  ASN A 494 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.22   27.78     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  THR B 368 "
           pdb=" C   THR B 368 "
           pdb=" N   GLN B 369 "
           pdb=" CA  GLN B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.15   26.85     0      5.00e+00 4.00e-02 2.88e+01
  ... (remaining 5563 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1060
       0.052 -    0.104: 262
       0.104 -    0.156: 48
       0.156 -    0.208: 14
       0.208 -    0.259: 4
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CA  PHE B 496 "
            pdb=" N   PHE B 496 "
            pdb=" C   PHE B 496 "
            pdb=" CB  PHE B 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  PHE A 496 "
            pdb=" N   PHE A 496 "
            pdb=" C   PHE A 496 "
            pdb=" CB  PHE A 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ILE A 303 "
            pdb=" N   ILE A 303 "
            pdb=" C   ILE A 303 "
            pdb=" CB  ILE A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1385 not shown)

  Planarity restraints: 1596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 549 "   -0.020 2.00e-02 2.50e+03   3.99e-02 1.59e+01
        pdb=" C   GLU B 549 "    0.069 2.00e-02 2.50e+03
        pdb=" O   GLU B 549 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ALA B 550 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 549 "   -0.020 2.00e-02 2.50e+03   3.98e-02 1.59e+01
        pdb=" C   GLU A 549 "    0.069 2.00e-02 2.50e+03
        pdb=" O   GLU A 549 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ALA A 550 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 548 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.30e+00
        pdb=" C   VAL B 548 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   VAL B 548 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLU B 549 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1593 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 135
        2.61 -     3.18: 9451
        3.18 -     3.76: 14198
        3.76 -     4.33: 20206
        4.33 -     4.90: 31744
  Nonbonded interactions: 75734
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 222 "
            pdb=" OE1 GLN A 369 "
     model   vdw
     2.041 3.040
  nonbonded pdb=" OD2 ASP A 467 "
            pdb=" O2B FAD A 701 "
     model   vdw
     2.061 3.040
  nonbonded pdb=" OH  TYR A 202 "
            pdb=" OD1 ASN A 322 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" OH  TYR B 202 "
            pdb=" OD1 ASN B 322 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" NZ  LYS A 420 "
            pdb=" OD1 ASN A 466 "
     model   vdw
     2.154 3.120
  ... (remaining 75729 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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 group one per residue
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:             8.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.670
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
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      :  0.006   0.110   9192  Z= 0.289
  Angle     :  0.892  13.771  12400  Z= 0.505
  Chirality :  0.050   0.259   1388
  Planarity :  0.011   0.088   1596
  Dihedral  : 14.977 110.531   3454
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.45 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.92 (0.23), residues: 1174
  helix: -1.38 (0.17), residues: 668
  sheet: -1.29 (0.54), residues: 72
  loop : -0.76 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.004   ARG B 163 
 TYR   0.016   0.005   TYR A 577 
 PHE   0.046   0.004   PHE A 496 
 TRP   0.016   0.005   TRP A 250 
 HIS   0.014   0.003   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00582 ( 9192)
  covalent geometry    : angle       0.89246 (12400)
  hydrogen bonds       : bond        0.16595 (  569)
  hydrogen bonds       : angle       7.48130 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 LEU cc_start: 0.9019 (mm) cc_final: 0.8812 (mt)
REVERT: A  382 GLU cc_start: 0.8364 (pp20) cc_final: 0.8021 (pp20)
REVERT: A  410 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7323 (tptt)
REVERT: A  438 MET cc_start: 0.8767 (mmm) cc_final: 0.8060 (mmm)
REVERT: A  479 MET cc_start: 0.8531 (mmp) cc_final: 0.8111 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0921
  time to fit residues: 12.8610
Evaluate side-chains
  68 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:   20.0000
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
B 183 GLN
B 369 GLN
B 599 HIS
A  87 GLN
A 183 GLN
A 599 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.075231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.066064 restraints weight = 32212.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.068034 restraints weight = 16570.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.069449 restraints weight = 10223.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.070461 restraints weight = 6911.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.071200 restraints weight = 5023.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9192  Z= 0.160
  Angle     :  0.646   7.956  12400  Z= 0.340
  Chirality :  0.043   0.156   1388
  Planarity :  0.004   0.036   1596
  Dihedral  :  9.074  78.638   1346
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.45 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  6.26 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.24), residues: 1174
  helix:  0.99 (0.19), residues: 688
  sheet: -0.05 (0.59), residues: 56
  loop : -0.34 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 205 
 TYR   0.014   0.001   TYR A 202 
 PHE   0.014   0.001   PHE B 443 
 TRP   0.013   0.002   TRP B 250 
 HIS   0.005   0.001   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9192)
  covalent geometry    : angle       0.64603 (12400)
  hydrogen bonds       : bond        0.05530 (  569)
  hydrogen bonds       : angle       4.78550 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  382 GLU cc_start: 0.8703 (pt0) cc_final: 0.8171 (pp20)
REVERT: B  438 MET cc_start: 0.8943 (mmm) cc_final: 0.8275 (mmm)
REVERT: B  503 MET cc_start: 0.5259 (mmt) cc_final: 0.2790 (tmm)
REVERT: A   87 GLN cc_start: 0.7404 (mt0) cc_final: 0.7203 (mt0)
REVERT: A  382 GLU cc_start: 0.8662 (pp20) cc_final: 0.8420 (pp20)
REVERT: A  438 MET cc_start: 0.9056 (mmm) cc_final: 0.8204 (mmm)
REVERT: A  479 MET cc_start: 0.8489 (mmp) cc_final: 0.8075 (mmt)
  outliers start: 9
  outliers final: 4
  residues processed: 95
  average time/residue: 0.0842
  time to fit residues: 12.2164
Evaluate side-chains
  75 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 107 optimal weight:    6.9990
   chunk 82 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 69 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 84 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN
B 375 HIS
A 369 GLN
A 375 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.072168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.063078 restraints weight = 32683.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.064974 restraints weight = 17017.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.066354 restraints weight = 10548.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.067370 restraints weight = 7160.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.068064 restraints weight = 5243.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   9192  Z= 0.269
  Angle     :  0.722  13.692  12400  Z= 0.371
  Chirality :  0.044   0.162   1388
  Planarity :  0.004   0.039   1596
  Dihedral  :  8.875  57.996   1346
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.73 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  9.34 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.24), residues: 1174
  helix:  1.33 (0.19), residues: 674
  sheet:  0.16 (0.53), residues: 60
  loop : -0.43 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 386 
 TYR   0.017   0.002   TYR B 161 
 PHE   0.016   0.002   PHE A 422 
 TRP   0.010   0.002   TRP A 250 
 HIS   0.014   0.002   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 9192)
  covalent geometry    : angle       0.72161 (12400)
  hydrogen bonds       : bond        0.05610 (  569)
  hydrogen bonds       : angle       4.79037 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  382 GLU cc_start: 0.8777 (pt0) cc_final: 0.8057 (pp20)
REVERT: B  503 MET cc_start: 0.5452 (mmt) cc_final: 0.3281 (tmm)
REVERT: A  382 GLU cc_start: 0.8613 (pp20) cc_final: 0.8291 (pp20)
REVERT: A  438 MET cc_start: 0.9041 (mmm) cc_final: 0.8370 (mmm)
REVERT: A  479 MET cc_start: 0.8467 (mmp) cc_final: 0.8002 (mmt)
REVERT: A  583 LEU cc_start: 0.8996 (mt) cc_final: 0.8699 (tt)
  outliers start: 18
  outliers final: 10
  residues processed: 89
  average time/residue: 0.0834
  time to fit residues: 11.2592
Evaluate side-chains
  77 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 14 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.074003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.064956 restraints weight = 32535.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.066867 restraints weight = 16641.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.068213 restraints weight = 10213.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.069230 restraints weight = 7012.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.069975 restraints weight = 5107.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9192  Z= 0.159
  Angle     :  0.613  12.851  12400  Z= 0.310
  Chirality :  0.041   0.235   1388
  Planarity :  0.004   0.033   1596
  Dihedral  :  8.603  57.008   1346
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.21 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 10.83 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.25), residues: 1174
  helix:  1.66 (0.20), residues: 678
  sheet:  0.19 (0.55), residues: 60
  loop : -0.20 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 205 
 TYR   0.010   0.001   TYR A 202 
 PHE   0.012   0.001   PHE A 422 
 TRP   0.006   0.001   TRP A 607 
 HIS   0.009   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9192)
  covalent geometry    : angle       0.61280 (12400)
  hydrogen bonds       : bond        0.04888 (  569)
  hydrogen bonds       : angle       4.32534 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 THR cc_start: 0.8863 (m) cc_final: 0.8127 (p)
REVERT: B  382 GLU cc_start: 0.8770 (pt0) cc_final: 0.8180 (pp20)
REVERT: B  503 MET cc_start: 0.5365 (mmt) cc_final: 0.3835 (tmm)
REVERT: B  583 LEU cc_start: 0.8970 (mt) cc_final: 0.8685 (tt)
REVERT: A  218 THR cc_start: 0.8894 (m) cc_final: 0.8163 (p)
REVERT: A  382 GLU cc_start: 0.8627 (pp20) cc_final: 0.8422 (pp20)
REVERT: A  438 MET cc_start: 0.8994 (mmm) cc_final: 0.8331 (mmm)
REVERT: A  479 MET cc_start: 0.8424 (mmp) cc_final: 0.7990 (mmt)
REVERT: A  583 LEU cc_start: 0.8917 (mt) cc_final: 0.8590 (tt)
  outliers start: 21
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0723
  time to fit residues: 10.6886
Evaluate side-chains
  84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  437 ILE
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0970
   chunk 46 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0020
   chunk 79 optimal weight:    9.9990
   chunk 72 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9980
   chunk 43 optimal weight:    9.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.075444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.066212 restraints weight = 32399.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.068358 restraints weight = 16281.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.069709 restraints weight = 9661.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.070553 restraints weight = 6485.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.071380 restraints weight = 4879.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9192  Z= 0.126
  Angle     :  0.562  11.928  12400  Z= 0.282
  Chirality :  0.040   0.250   1388
  Planarity :  0.003   0.030   1596
  Dihedral  :  8.371  57.116   1346
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.36 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.25), residues: 1174
  helix:  1.94 (0.20), residues: 678
  sheet:  0.54 (0.62), residues: 56
  loop : -0.06 (0.33), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 205 
 TYR   0.007   0.001   TYR B 202 
 PHE   0.012   0.001   PHE B 409 
 TRP   0.006   0.001   TRP B 607 
 HIS   0.008   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9192)
  covalent geometry    : angle       0.56230 (12400)
  hydrogen bonds       : bond        0.04446 (  569)
  hydrogen bonds       : angle       4.02138 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 THR cc_start: 0.8845 (m) cc_final: 0.8092 (p)
REVERT: B  301 MET cc_start: 0.8288 (mmm) cc_final: 0.7927 (mmm)
REVERT: B  382 GLU cc_start: 0.8818 (pt0) cc_final: 0.7988 (pp20)
REVERT: B  503 MET cc_start: 0.5311 (mmt) cc_final: 0.4094 (tmm)
REVERT: A  218 THR cc_start: 0.8845 (m) cc_final: 0.8094 (p)
REVERT: A  382 GLU cc_start: 0.8705 (pp20) cc_final: 0.8438 (pp20)
REVERT: A  438 MET cc_start: 0.8995 (mmm) cc_final: 0.8245 (mmm)
REVERT: A  467 ASP cc_start: 0.8605 (p0) cc_final: 0.8366 (m-30)
REVERT: A  479 MET cc_start: 0.8400 (mmp) cc_final: 0.7977 (mmt)
REVERT: A  583 LEU cc_start: 0.8959 (mt) cc_final: 0.8672 (tt)
  outliers start: 21
  outliers final: 13
  residues processed: 96
  average time/residue: 0.0743
  time to fit residues: 11.1026
Evaluate side-chains
  86 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  405 MET
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   chunk 112 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0170
   chunk 67 optimal weight:    3.9990
   chunk 100 optimal weight:   20.0000
   chunk 94 optimal weight:    8.9990
   chunk 96 optimal weight:    4.9990
   chunk 8 optimal weight:    0.3980
   chunk 24 optimal weight:    7.9990
   overall best weight:    1.8824

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

Flipped N/Q/H residues before XYZ refinement:
B 363 HIS
B 369 GLN
B 498 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.075709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.066514 restraints weight = 32355.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.068573 restraints weight = 16398.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.070010 restraints weight = 9918.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.070986 restraints weight = 6626.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.071611 restraints weight = 4825.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9192  Z= 0.132
  Angle     :  0.564  11.062  12400  Z= 0.283
  Chirality :  0.040   0.196   1388
  Planarity :  0.003   0.032   1596
  Dihedral  :  8.232  58.250   1346
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.42 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.26), residues: 1174
  helix:  2.07 (0.20), residues: 680
  sheet: -0.42 (0.59), residues: 72
  loop :  0.24 (0.34), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 205 
 TYR   0.007   0.001   TYR A 399 
 PHE   0.012   0.001   PHE A 422 
 TRP   0.006   0.001   TRP B 607 
 HIS   0.008   0.002   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9192)
  covalent geometry    : angle       0.56403 (12400)
  hydrogen bonds       : bond        0.04375 (  569)
  hydrogen bonds       : angle       3.99518 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 THR cc_start: 0.8863 (m) cc_final: 0.8134 (p)
REVERT: B  301 MET cc_start: 0.8383 (mmm) cc_final: 0.8054 (mmm)
REVERT: B  382 GLU cc_start: 0.8774 (pt0) cc_final: 0.8053 (pp20)
REVERT: B  400 MET cc_start: 0.8997 (ttt) cc_final: 0.8650 (ttt)
REVERT: B  503 MET cc_start: 0.5217 (mmt) cc_final: 0.4014 (tmm)
REVERT: A  218 THR cc_start: 0.8856 (m) cc_final: 0.8114 (p)
REVERT: A  382 GLU cc_start: 0.8742 (pp20) cc_final: 0.8455 (pp20)
REVERT: A  438 MET cc_start: 0.8990 (mmm) cc_final: 0.8261 (mmm)
REVERT: A  479 MET cc_start: 0.8383 (mmp) cc_final: 0.8003 (mmt)
REVERT: A  583 LEU cc_start: 0.8958 (mt) cc_final: 0.8708 (tt)
  outliers start: 24
  outliers final: 18
  residues processed: 93
  average time/residue: 0.0778
  time to fit residues: 11.1137
Evaluate side-chains
  92 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  353 MET
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 92 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.075812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.066489 restraints weight = 32576.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.068506 restraints weight = 16551.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.069991 restraints weight = 10077.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.071010 restraints weight = 6676.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.071676 restraints weight = 4860.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9192  Z= 0.127
  Angle     :  0.540  10.686  12400  Z= 0.272
  Chirality :  0.039   0.182   1388
  Planarity :  0.003   0.034   1596
  Dihedral  :  8.073  58.407   1346
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.21 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.26), residues: 1174
  helix:  2.15 (0.20), residues: 680
  sheet: -0.45 (0.59), residues: 72
  loop :  0.34 (0.34), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 532 
 TYR   0.007   0.001   TYR B 399 
 PHE   0.013   0.001   PHE A 409 
 TRP   0.007   0.001   TRP B 607 
 HIS   0.007   0.001   HIS B 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9192)
  covalent geometry    : angle       0.54044 (12400)
  hydrogen bonds       : bond        0.04280 (  569)
  hydrogen bonds       : angle       3.93402 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.380 
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: B  218 THR cc_start: 0.8844 (m) cc_final: 0.8115 (p)
REVERT: B  380 ILE cc_start: 0.9425 (mp) cc_final: 0.9017 (mt)
REVERT: B  382 GLU cc_start: 0.8765 (pt0) cc_final: 0.7920 (pp20)
REVERT: B  400 MET cc_start: 0.9000 (ttt) cc_final: 0.8671 (ttt)
REVERT: B  503 MET cc_start: 0.5334 (mmt) cc_final: 0.4139 (tmm)
REVERT: A  218 THR cc_start: 0.8875 (m) cc_final: 0.8126 (p)
REVERT: A  301 MET cc_start: 0.8354 (mmm) cc_final: 0.8001 (mmm)
REVERT: A  382 GLU cc_start: 0.8734 (pp20) cc_final: 0.8452 (pp20)
REVERT: A  438 MET cc_start: 0.8989 (mmm) cc_final: 0.8359 (mmm)
REVERT: A  467 ASP cc_start: 0.8371 (m-30) cc_final: 0.7796 (p0)
REVERT: A  479 MET cc_start: 0.8353 (mmp) cc_final: 0.7990 (mmt)
  outliers start: 22
  outliers final: 17
  residues processed: 97
  average time/residue: 0.0784
  time to fit residues: 11.7455
Evaluate side-chains
  95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  353 MET
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 46 optimal weight:    4.9990
   chunk 115 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 114 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.075497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.066327 restraints weight = 32269.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.068217 restraints weight = 16473.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.069661 restraints weight = 10179.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.070717 restraints weight = 6905.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.071335 restraints weight = 4983.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9192  Z= 0.138
  Angle     :  0.550  10.213  12400  Z= 0.279
  Chirality :  0.040   0.160   1388
  Planarity :  0.003   0.032   1596
  Dihedral  :  7.967  58.860   1346
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.53 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.26), residues: 1174
  helix:  2.23 (0.20), residues: 692
  sheet: -0.32 (0.60), residues: 72
  loop :  0.35 (0.35), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 532 
 TYR   0.007   0.001   TYR A 399 
 PHE   0.011   0.001   PHE B 422 
 TRP   0.006   0.001   TRP B 607 
 HIS   0.008   0.002   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9192)
  covalent geometry    : angle       0.55044 (12400)
  hydrogen bonds       : bond        0.04345 (  569)
  hydrogen bonds       : angle       3.96439 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 THR cc_start: 0.8852 (m) cc_final: 0.8123 (p)
REVERT: B  380 ILE cc_start: 0.9443 (mp) cc_final: 0.9039 (mt)
REVERT: B  382 GLU cc_start: 0.8763 (pt0) cc_final: 0.7907 (pp20)
REVERT: B  400 MET cc_start: 0.8979 (ttt) cc_final: 0.8664 (ttt)
REVERT: B  503 MET cc_start: 0.5303 (mmt) cc_final: 0.4062 (tmm)
REVERT: A  218 THR cc_start: 0.8885 (m) cc_final: 0.8138 (p)
REVERT: A  382 GLU cc_start: 0.8754 (pp20) cc_final: 0.8503 (pp20)
REVERT: A  438 MET cc_start: 0.8984 (mmm) cc_final: 0.8354 (mmm)
REVERT: A  479 MET cc_start: 0.8342 (mmp) cc_final: 0.8001 (mmt)
  outliers start: 23
  outliers final: 21
  residues processed: 95
  average time/residue: 0.0770
  time to fit residues: 11.3549
Evaluate side-chains
  97 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  353 MET
Chi-restraints excluded: chain B residue  369 GLN
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  475 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  401 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 106 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9980
   chunk 114 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 107 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN
A 363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.076758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.067515 restraints weight = 31969.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.069552 restraints weight = 16318.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.070984 restraints weight = 9955.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.071891 restraints weight = 6663.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.072646 restraints weight = 4943.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9192  Z= 0.112
  Angle     :  0.539   9.985  12400  Z= 0.269
  Chirality :  0.039   0.158   1388
  Planarity :  0.003   0.034   1596
  Dihedral  :  7.871  57.640   1346
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.63 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.26), residues: 1174
  helix:  2.22 (0.19), residues: 706
  sheet: -0.16 (0.61), residues: 72
  loop :  0.42 (0.36), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 367 
 TYR   0.006   0.001   TYR A 399 
 PHE   0.011   0.001   PHE B 422 
 TRP   0.007   0.001   TRP A 607 
 HIS   0.006   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9192)
  covalent geometry    : angle       0.53938 (12400)
  hydrogen bonds       : bond        0.04109 (  569)
  hydrogen bonds       : angle       3.86192 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   80 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8668 (tptt)
REVERT: B  218 THR cc_start: 0.8802 (m) cc_final: 0.8068 (p)
REVERT: B  380 ILE cc_start: 0.9437 (mp) cc_final: 0.9045 (mt)
REVERT: B  382 GLU cc_start: 0.8707 (pt0) cc_final: 0.7949 (pp20)
REVERT: B  400 MET cc_start: 0.8912 (ttt) cc_final: 0.8640 (ttt)
REVERT: B  503 MET cc_start: 0.5178 (mmt) cc_final: 0.4212 (tmm)
REVERT: A  218 THR cc_start: 0.8852 (m) cc_final: 0.8103 (p)
REVERT: A  301 MET cc_start: 0.8377 (mmm) cc_final: 0.8125 (mmm)
REVERT: A  382 GLU cc_start: 0.8767 (pp20) cc_final: 0.8468 (pp20)
REVERT: A  438 MET cc_start: 0.8892 (mmm) cc_final: 0.8296 (mmm)
  outliers start: 20
  outliers final: 15
  residues processed: 103
  average time/residue: 0.0795
  time to fit residues: 12.5149
Evaluate side-chains
  94 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  353 MET
Chi-restraints excluded: chain B residue  369 GLN
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 113 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 55 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.076915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.067629 restraints weight = 31912.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.069573 restraints weight = 16298.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.071049 restraints weight = 10082.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.071907 restraints weight = 6808.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.072710 restraints weight = 5170.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.4114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9192  Z= 0.115
  Angle     :  0.556   9.745  12400  Z= 0.274
  Chirality :  0.040   0.159   1388
  Planarity :  0.003   0.036   1596
  Dihedral  :  7.760  57.527   1346
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.59 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.26), residues: 1174
  helix:  2.30 (0.19), residues: 706
  sheet: -0.07 (0.61), residues: 72
  loop :  0.44 (0.36), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 205 
 TYR   0.006   0.001   TYR A 399 
 PHE   0.011   0.001   PHE B 422 
 TRP   0.008   0.001   TRP A 607 
 HIS   0.006   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9192)
  covalent geometry    : angle       0.55550 (12400)
  hydrogen bonds       : bond        0.04115 (  569)
  hydrogen bonds       : angle       3.82150 ( 1647)

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

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

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2348 Ramachandran restraints generated.
    1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.336 
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: B  218 THR cc_start: 0.8843 (m) cc_final: 0.8110 (p)
REVERT: B  380 ILE cc_start: 0.9432 (mp) cc_final: 0.9057 (mt)
REVERT: B  382 GLU cc_start: 0.8720 (pt0) cc_final: 0.7950 (pp20)
REVERT: B  400 MET cc_start: 0.8918 (ttt) cc_final: 0.8643 (ttt)
REVERT: B  438 MET cc_start: 0.8587 (mtp) cc_final: 0.8347 (ttp)
REVERT: B  503 MET cc_start: 0.5305 (mmt) cc_final: 0.4544 (tmm)
REVERT: A  218 THR cc_start: 0.8841 (m) cc_final: 0.8089 (p)
REVERT: A  301 MET cc_start: 0.8319 (mmm) cc_final: 0.8071 (mmm)
REVERT: A  382 GLU cc_start: 0.8746 (pp20) cc_final: 0.8446 (pp20)
REVERT: A  438 MET cc_start: 0.8879 (mmm) cc_final: 0.8370 (mmm)
  outliers start: 17
  outliers final: 15
  residues processed: 98
  average time/residue: 0.0875
  time to fit residues: 12.8856
Evaluate side-chains
  99 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  345 MET
Chi-restraints excluded: chain B residue  353 MET
Chi-restraints excluded: chain B residue  450 GLU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain A residue   78 MET
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  488 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0470
   chunk 17 optimal weight:    8.9990
   chunk 83 optimal weight:    0.4980
   chunk 115 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 58 optimal weight:   20.0000
   chunk 15 optimal weight:    0.4980
   overall best weight:    0.5880

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

Flipped N/Q/H residues before XYZ refinement:
B 118 ASN
B 307 ASN
B 369 GLN
A 118 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.082667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.073446 restraints weight = 31837.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.075388 restraints weight = 16954.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.076657 restraints weight = 10625.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.077677 restraints weight = 7420.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.078353 restraints weight = 5532.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.4417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9192  Z= 0.102
  Angle     :  0.550   9.474  12400  Z= 0.268
  Chirality :  0.039   0.165   1388
  Planarity :  0.003   0.037   1596
  Dihedral  :  7.577  57.356   1346
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.01 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.26), residues: 1174
  helix:  2.43 (0.19), residues: 706
  sheet:  0.07 (0.62), residues: 72
  loop :  0.48 (0.36), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 532 
 TYR   0.005   0.001   TYR A 399 
 PHE   0.011   0.001   PHE B 422 
 TRP   0.010   0.001   TRP B 250 
 HIS   0.005   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 9192)
  covalent geometry    : angle       0.55024 (12400)
  hydrogen bonds       : bond        0.03807 (  569)
  hydrogen bonds       : angle       3.72354 ( 1647)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1309.17 seconds
wall clock time: 23 minutes 42.36 seconds (1422.36 seconds total)