Starting phenix.real_space_refine
on Tue Mar  3 20:18:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i39_35146/03_2026/8i39_35146_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i39_35146/03_2026/8i39_35146.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i39_35146/03_2026/8i39_35146_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i39_35146/03_2026/8i39_35146_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i39_35146/03_2026/8i39_35146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i39_35146/03_2026/8i39_35146.map"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.184
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: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5495      2.51       5
     N    1398      2.21       5
     O    1470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8413
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 538, 4197
          Classifications: {'peptide': 538}
          Link IDs: {'PTRANS': 17, 'TRANS': 520}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 538, 4197
          Classifications: {'peptide': 538}
          Link IDs: {'PTRANS': 17, 'TRANS': 520}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'A8S': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.28, per 1000 atoms: 0.27
  Number of scatterers: 8413
  At special positions: 0
  Unit cell: (77.35, 103.53, 119, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1470      8.00
     N    1398      7.00
     C    5495      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: 0.67
  Conformation dependent library (CDL) restraints added in 308.4 milliseconds
  

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1980

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      50.2% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 115
      removed outlier: 3.541A  pdb=" N   LEU A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ALA A 113 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 169
      removed outlier: 3.595A  pdb=" N   LEU A 161 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 164 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 189
    Processing helix  chain 'A' and resid 191 through 195
      removed outlier: 3.986A  pdb=" N   GLU A 195 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 219
      removed outlier: 3.618A  pdb=" N   SER A 216 " --> pdb=" O   ARG A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 255
      removed outlier: 3.809A  pdb=" N   VAL A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ALA A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 274
      removed outlier: 3.543A  pdb=" N   GLN A 273 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 300
      removed outlier: 4.728A  pdb=" N   MET A 296 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   ALA A 297 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   GLU A 300 " --> pdb=" O   MET A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 322
    Processing helix  chain 'A' and resid 338 through 344
      removed outlier: 3.634A  pdb=" N   THR A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 397
      removed outlier: 3.961A  pdb=" N   PHE A 387 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS A 391 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 403
      removed outlier: 3.585A  pdb=" N   ARG A 402 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   HIS A 403 " --> pdb=" O   GLU A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 416 through 421
    Processing helix  chain 'A' and resid 432 through 437
    Processing helix  chain 'A' and resid 438 through 455
      removed outlier: 3.914A  pdb=" N   GLY A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 462 through 472
      removed outlier: 3.745A  pdb=" N   SER A 472 " --> pdb=" O   ARG A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 492
      removed outlier: 4.031A  pdb=" N   SER A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   MET A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 500
      removed outlier: 3.524A  pdb=" N   SER A 498 " --> pdb=" O   VAL A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 541
      removed outlier: 3.874A  pdb=" N   LEU A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 551
      removed outlier: 3.766A  pdb=" N   ILE A 550 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 561
      removed outlier: 3.581A  pdb=" N   ALA A 557 " --> pdb=" O   VAL A 553 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR A 561 " --> pdb=" O   ALA A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 578
      removed outlier: 3.547A  pdb=" N   LYS A 577 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 594
      removed outlier: 3.538A  pdb=" N   CYS A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 658
      removed outlier: 3.576A  pdb=" N   ALA A 653 " --> pdb=" O   TYR A 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 115
      removed outlier: 3.541A  pdb=" N   LEU B 110 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   ALA B 113 " --> pdb=" O   THR B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 169
      removed outlier: 3.595A  pdb=" N   LEU B 161 " --> pdb=" O   VAL B 157 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL B 164 " --> pdb=" O   THR B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 189
    Processing helix  chain 'B' and resid 191 through 195
      removed outlier: 3.986A  pdb=" N   GLU B 195 " --> pdb=" O   THR B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 219
      removed outlier: 3.618A  pdb=" N   SER B 216 " --> pdb=" O   ARG B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 255
      removed outlier: 3.809A  pdb=" N   VAL B 246 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ALA B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 274
      removed outlier: 3.542A  pdb=" N   GLN B 273 " --> pdb=" O   SER B 269 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   MET B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 300
      removed outlier: 4.728A  pdb=" N   MET B 296 " --> pdb=" O   GLY B 292 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ALA B 297 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   GLU B 300 " --> pdb=" O   MET B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 322
    Processing helix  chain 'B' and resid 338 through 344
      removed outlier: 3.634A  pdb=" N   THR B 343 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA B 344 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 397
      removed outlier: 3.961A  pdb=" N   PHE B 387 " --> pdb=" O   ILE B 383 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS B 391 " --> pdb=" O   PHE B 387 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU B 397 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 403
      removed outlier: 3.586A  pdb=" N   ARG B 402 " --> pdb=" O   LYS B 399 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   HIS B 403 " --> pdb=" O   GLU B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 416 through 421
    Processing helix  chain 'B' and resid 432 through 437
    Processing helix  chain 'B' and resid 438 through 455
      removed outlier: 3.914A  pdb=" N   GLY B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
      Proline residue:  B 451  - end of helix
    Processing helix  chain 'B' and resid 459 through 461
      No H-bonds generated for 'chain 'B' and resid 459 through 461'
    Processing helix  chain 'B' and resid 462 through 472
      removed outlier: 3.745A  pdb=" N   SER B 472 " --> pdb=" O   ARG B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 492
      removed outlier: 4.031A  pdb=" N   SER B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   MET B 491 " --> pdb=" O   GLY B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 500
      removed outlier: 3.524A  pdb=" N   SER B 498 " --> pdb=" O   VAL B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 541
      removed outlier: 3.875A  pdb=" N   LEU B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 551
      removed outlier: 3.766A  pdb=" N   ILE B 550 " --> pdb=" O   LYS B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 561
      removed outlier: 3.581A  pdb=" N   ALA B 557 " --> pdb=" O   VAL B 553 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR B 561 " --> pdb=" O   ALA B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 578
      removed outlier: 3.547A  pdb=" N   LYS B 577 " --> pdb=" O   VAL B 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 581 through 594
      removed outlier: 3.538A  pdb=" N   CYS B 585 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLN B 593 " --> pdb=" O   LEU B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 658
      removed outlier: 3.576A  pdb=" N   ALA B 653 " --> pdb=" O   TYR B 649 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88
      removed outlier: 5.317A  pdb=" N   SER A  85 " --> pdb=" O   TYR A  47 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   TYR A  47 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ASP A  44 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   LYS A 126 " --> pdb=" O   ASP A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145
      removed outlier: 6.141A  pdb=" N   GLY A 143 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ASP A 231 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   VAL A 145 " --> pdb=" O   ASP A 231 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU A 228 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   SER A 263 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   LEU A 230 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   MET A  97 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 88
      removed outlier: 5.316A  pdb=" N   SER B  85 " --> pdb=" O   TYR B  47 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   TYR B  47 " --> pdb=" O   SER B  85 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ASP B  44 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   LYS B 126 " --> pdb=" O   ASP B  44 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145
      removed outlier: 6.140A  pdb=" N   GLY B 143 " --> pdb=" O   VAL B 229 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ASP B 231 " --> pdb=" O   GLY B 143 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   VAL B 145 " --> pdb=" O   ASP B 231 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU B 228 " --> pdb=" O   VAL B 261 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   SER B 263 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   LEU B 230 " --> pdb=" O   SER B 263 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   MET B  97 " --> pdb=" O   THR B 262 " (cutoff:3.500A)

    290 hydrogen bonds defined for protein.
    840 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: 1.06

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1279
        1.30 -     1.42: 2251
        1.42 -     1.55: 4961
        1.55 -     1.68: 12
        1.68 -     1.81: 84
  Bond restraints: 8587
  Sorted by residual:
  bond pdb=" C1  A8S B 701 "
       pdb=" O11 A8S B 701 "
    ideal  model  delta    sigma   weight residual
    1.250  1.167  0.083 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" C3  A8S B 701 "
       pdb=" C4  A8S B 701 "
    ideal  model  delta    sigma   weight residual
    1.463  1.381  0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" C1  A8S B 701 "
       pdb=" O12 A8S B 701 "
    ideal  model  delta    sigma   weight residual
    1.249  1.173  0.076 2.00e-02 2.50e+03 1.45e+01
  bond pdb=" C1  A8S B 701 "
       pdb=" C2  A8S B 701 "
    ideal  model  delta    sigma   weight residual
    1.512  1.457  0.055 2.00e-02 2.50e+03 7.63e+00
  bond pdb=" CB  GLU A 183 "
       pdb=" CG  GLU A 183 "
    ideal  model  delta    sigma   weight residual
    1.520  1.595 -0.075 3.00e-02 1.11e+03 6.29e+00
  ... (remaining 8582 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 11506
        2.94 -     5.87: 108
        5.87 -     8.81: 16
        8.81 -    11.75: 5
       11.75 -    14.68: 6
  Bond angle restraints: 11641
  Sorted by residual:
  angle pdb=" CA  GLU B 183 "
        pdb=" CB  GLU B 183 "
        pdb=" CG  GLU B 183 "
      ideal   model   delta    sigma   weight residual
     114.10  128.78  -14.68 2.00e+00 2.50e-01 5.39e+01
  angle pdb=" CA  GLU A 183 "
        pdb=" CB  GLU A 183 "
        pdb=" CG  GLU A 183 "
      ideal   model   delta    sigma   weight residual
     114.10  128.74  -14.64 2.00e+00 2.50e-01 5.36e+01
  angle pdb=" CA  GLU A 188 "
        pdb=" CB  GLU A 188 "
        pdb=" CG  GLU A 188 "
      ideal   model   delta    sigma   weight residual
     114.10  127.95  -13.85 2.00e+00 2.50e-01 4.79e+01
  angle pdb=" CA  GLU B 188 "
        pdb=" CB  GLU B 188 "
        pdb=" CG  GLU B 188 "
      ideal   model   delta    sigma   weight residual
     114.10  127.94  -13.84 2.00e+00 2.50e-01 4.79e+01
  angle pdb=" N   HIS A 403 "
        pdb=" CA  HIS A 403 "
        pdb=" C   HIS A 403 "
      ideal   model   delta    sigma   weight residual
     114.04  105.48    8.56 1.24e+00 6.50e-01 4.77e+01
  ... (remaining 11636 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.95: 4722
       19.95 -    39.91: 275
       39.91 -    59.86: 40
       59.86 -    79.81: 9
       79.81 -    99.76: 12
  Dihedral angle restraints: 5058
    sinusoidal: 1976
      harmonic: 3082
  Sorted by residual:
  dihedral pdb=" CA  MET B 310 "
           pdb=" C   MET B 310 "
           pdb=" N   ASN B 311 "
           pdb=" CA  ASN B 311 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.46   23.54     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  MET A 310 "
           pdb=" C   MET A 310 "
           pdb=" N   ASN A 311 "
           pdb=" CA  ASN A 311 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.49   23.51     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  LYS A 133 "
           pdb=" C   LYS A 133 "
           pdb=" N   ILE A 134 "
           pdb=" CA  ILE A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.72  -22.28     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 5055 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1222
       0.073 -    0.146: 156
       0.146 -    0.219: 8
       0.219 -    0.292: 0
       0.292 -    0.364: 1
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" C7  A8S B 701 "
            pdb=" C12 A8S B 701 "
            pdb=" C8  A8S B 701 "
            pdb=" O7  A8S B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.32   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" CA  GLU A 188 "
            pdb=" N   GLU A 188 "
            pdb=" C   GLU A 188 "
            pdb=" CB  GLU A 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.83e-01
  chirality pdb=" CA  GLU B 188 "
            pdb=" N   GLU B 188 "
            pdb=" C   GLU B 188 "
            pdb=" CB  GLU B 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.81e-01
  ... (remaining 1384 not shown)

  Planarity restraints: 1424
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  A8S B 701 "   -0.244 2.00e-02 2.50e+03   2.51e-01 6.31e+02
        pdb=" C4  A8S B 701 "    0.202 2.00e-02 2.50e+03
        pdb=" C5  A8S B 701 "    0.296 2.00e-02 2.50e+03
        pdb=" C7  A8S B 701 "   -0.254 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  A8S B 701 "   -0.128 2.00e-02 2.50e+03   1.07e-01 1.42e+02
        pdb=" C2  A8S B 701 "    0.175 2.00e-02 2.50e+03
        pdb=" C3  A8S B 701 "    0.030 2.00e-02 2.50e+03
        pdb=" C4  A8S B 701 "    0.016 2.00e-02 2.50e+03
        pdb=" C6  A8S B 701 "   -0.094 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 450 "    0.045 5.00e-02 4.00e+02   6.74e-02 7.26e+00
        pdb=" N   PRO B 451 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1421 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 138
        2.67 -     3.23: 8252
        3.23 -     3.79: 11946
        3.79 -     4.34: 19065
        4.34 -     4.90: 29642
  Nonbonded interactions: 69043
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 298 "
            pdb=" OG  SER B 301 "
     model   vdw
     2.116 3.040
  nonbonded pdb=" O   TYR A 298 "
            pdb=" OG  SER A 301 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" O   PRO A 102 "
            pdb=" OG  SER A 105 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   PRO B 102 "
            pdb=" OG  SER B 105 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" OE2 GLU B 300 "
            pdb=" OG  SER B 305 "
     model   vdw
     2.209 3.040
  ... (remaining 69038 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 36 through 660)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.600
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
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      :  0.009   0.083   8587  Z= 0.371
  Angle     :  0.901  14.682  11641  Z= 0.504
  Chirality :  0.050   0.364   1387
  Planarity :  0.009   0.251   1424
  Dihedral  : 14.167  99.764   3078
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 22.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.81 %
    Favored  : 94.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -5.71 (0.19), residues: 1056
  helix: -4.67 (0.10), residues: 572
  sheet: -2.41 (0.57), residues: 56
  loop : -2.36 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  48 
 TYR   0.027   0.003   TYR A 475 
 PHE   0.028   0.002   PHE B 499 
 TRP   0.018   0.003   TRP A 426 
 HIS   0.011   0.003   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00867 ( 8587)
  covalent geometry    : angle       0.90088 (11641)
  hydrogen bonds       : bond        0.32277 (  290)
  hydrogen bonds       : angle      12.27655 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 MET cc_start: 0.7579 (ttm) cc_final: 0.7282 (ttm)
REVERT: A  148 ASP cc_start: 0.7773 (m-30) cc_final: 0.7547 (m-30)
REVERT: A  180 ARG cc_start: 0.7258 (mtp180) cc_final: 0.6950 (mtm180)
REVERT: A  224 ASN cc_start: 0.7914 (t0) cc_final: 0.7490 (t0)
REVERT: A  227 LEU cc_start: 0.8199 (tp) cc_final: 0.7943 (tp)
REVERT: A  424 MET cc_start: 0.7713 (mmm) cc_final: 0.7447 (mmm)
REVERT: A  430 TYR cc_start: 0.7900 (p90) cc_final: 0.7597 (p90)
REVERT: A  469 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7494 (mt-10)
REVERT: A  474 MET cc_start: 0.8257 (ttt) cc_final: 0.7957 (ttt)
REVERT: A  475 TYR cc_start: 0.8743 (p90) cc_final: 0.8529 (p90)
REVERT: A  555 MET cc_start: 0.8615 (mmm) cc_final: 0.8270 (mmm)
REVERT: A  568 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7568 (mmmt)
REVERT: B   97 MET cc_start: 0.7163 (ttm) cc_final: 0.6756 (ttm)
REVERT: B  139 LEU cc_start: 0.8547 (mt) cc_final: 0.8343 (tp)
REVERT: B  180 ARG cc_start: 0.7293 (mtp180) cc_final: 0.7017 (mtm180)
REVERT: B  270 ARG cc_start: 0.6542 (mtt180) cc_final: 0.6311 (mtt180)
REVERT: B  291 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7067 (tptp)
REVERT: B  430 TYR cc_start: 0.7819 (p90) cc_final: 0.7342 (p90)
REVERT: B  474 MET cc_start: 0.8242 (ttt) cc_final: 0.7922 (ttt)
REVERT: B  506 MET cc_start: 0.7258 (mtp) cc_final: 0.7027 (mtp)
REVERT: B  545 LYS cc_start: 0.7742 (mptt) cc_final: 0.7504 (pttm)
REVERT: B  555 MET cc_start: 0.8237 (mmm) cc_final: 0.7888 (mmm)
REVERT: B  568 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7812 (mmmt)
  outliers start: 2
  outliers final: 0
  residues processed: 148
  average time/residue: 0.5948
  time to fit residues: 93.2310
Evaluate side-chains
  114 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
A 321 ASN
A 454 ASN
B 130 ASN
B 321 ASN
B 325 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.182633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.133593 restraints weight = 8615.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 1.85
r_work: 0.3424 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8587  Z= 0.137
  Angle     :  0.615   5.287  11641  Z= 0.319
  Chirality :  0.042   0.131   1387
  Planarity :  0.005   0.038   1424
  Dihedral  :  6.802  45.911   1188
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  :  9.08 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -4.48 (0.22), residues: 1056
  helix: -3.29 (0.15), residues: 634
  sheet: -2.10 (0.55), residues: 76
  loop : -2.02 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 293 
 TYR   0.020   0.001   TYR B 475 
 PHE   0.021   0.001   PHE A 144 
 TRP   0.011   0.002   TRP B 447 
 HIS   0.006   0.001   HIS B 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8587)
  covalent geometry    : angle       0.61514 (11641)
  hydrogen bonds       : bond        0.03648 (  290)
  hydrogen bonds       : angle       5.47107 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6861 (tmm)
REVERT: A   97 MET cc_start: 0.6753 (ttm) cc_final: 0.6460 (ttm)
REVERT: A  148 ASP cc_start: 0.7804 (m-30) cc_final: 0.7545 (m-30)
REVERT: A  180 ARG cc_start: 0.7071 (mtp180) cc_final: 0.6673 (mtm180)
REVERT: A  232 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7122 (mt-10)
REVERT: A  291 LYS cc_start: 0.6462 (mmmt) cc_final: 0.5083 (ttpp)
REVERT: A  424 MET cc_start: 0.8120 (mmm) cc_final: 0.7919 (mmm)
REVERT: A  430 TYR cc_start: 0.7801 (p90) cc_final: 0.7594 (p90)
REVERT: A  469 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7429 (mt-10)
REVERT: A  474 MET cc_start: 0.8020 (ttt) cc_final: 0.7756 (ttt)
REVERT: A  475 TYR cc_start: 0.8393 (p90) cc_final: 0.8044 (p90)
REVERT: A  555 MET cc_start: 0.8631 (mmm) cc_final: 0.8283 (mmm)
REVERT: A  576 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7691 (ttm)
REVERT: B   97 MET cc_start: 0.6595 (ttm) cc_final: 0.6287 (ttm)
REVERT: B  158 ARG cc_start: 0.7336 (ttp80) cc_final: 0.7057 (ttp80)
REVERT: B  180 ARG cc_start: 0.6984 (mtp180) cc_final: 0.6492 (mtm180)
REVERT: B  291 LYS cc_start: 0.6633 (mmmt) cc_final: 0.6109 (tptp)
REVERT: B  395 HIS cc_start: 0.7548 (t-170) cc_final: 0.6357 (m90)
REVERT: B  430 TYR cc_start: 0.7795 (p90) cc_final: 0.7453 (p90)
REVERT: B  474 MET cc_start: 0.7724 (ttt) cc_final: 0.7493 (ttt)
REVERT: B  545 LYS cc_start: 0.7660 (mptt) cc_final: 0.6869 (pttm)
REVERT: B  555 MET cc_start: 0.8377 (mmm) cc_final: 0.8097 (mmm)
REVERT: B  658 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7393 (mtm180)
  outliers start: 21
  outliers final: 6
  residues processed: 153
  average time/residue: 0.5523
  time to fit residues: 89.7419
Evaluate side-chains
  134 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  571 SER
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Chi-restraints excluded: chain B residue  658 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 84 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 54 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   chunk 41 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B 454 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.181439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.120238 restraints weight = 8390.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.78
r_work: 0.3386 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8587  Z= 0.112
  Angle     :  0.547   5.990  11641  Z= 0.282
  Chirality :  0.040   0.142   1387
  Planarity :  0.004   0.037   1424
  Dihedral  :  5.097  24.636   1188
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 11.05 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -3.39 (0.23), residues: 1056
  helix: -2.20 (0.18), residues: 634
  sheet: -1.82 (0.54), residues: 80
  loop : -2.01 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 293 
 TYR   0.032   0.001   TYR B 475 
 PHE   0.020   0.001   PHE B  42 
 TRP   0.010   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8587)
  covalent geometry    : angle       0.54720 (11641)
  hydrogen bonds       : bond        0.03099 (  290)
  hydrogen bonds       : angle       4.61922 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.5461 (tt0) cc_final: 0.5211 (tt0)
REVERT: A   97 MET cc_start: 0.6547 (ttm) cc_final: 0.6223 (ttm)
REVERT: A  148 ASP cc_start: 0.7753 (m-30) cc_final: 0.7518 (m-30)
REVERT: A  158 ARG cc_start: 0.7295 (ttp80) cc_final: 0.6973 (ttp80)
REVERT: A  180 ARG cc_start: 0.7081 (mtp180) cc_final: 0.6633 (mtm180)
REVERT: A  188 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7570 (pp20)
REVERT: A  196 ASN cc_start: 0.8190 (m-40) cc_final: 0.7971 (m-40)
REVERT: A  280 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5765 (mm)
REVERT: A  291 LYS cc_start: 0.6065 (mmmt) cc_final: 0.5645 (tptp)
REVERT: A  430 TYR cc_start: 0.7709 (p90) cc_final: 0.7419 (p90)
REVERT: A  474 MET cc_start: 0.7822 (ttt) cc_final: 0.7591 (ttp)
REVERT: A  505 TRP cc_start: 0.8257 (m100) cc_final: 0.7847 (m100)
REVERT: A  555 MET cc_start: 0.8526 (mmm) cc_final: 0.8281 (mmp)
REVERT: A  587 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7629 (mmp-170)
REVERT: A  658 ARG cc_start: 0.7550 (ttt180) cc_final: 0.7331 (mmm160)
REVERT: B   97 MET cc_start: 0.6707 (ttm) cc_final: 0.6460 (ttm)
REVERT: B  180 ARG cc_start: 0.6915 (mtp180) cc_final: 0.6447 (mtm180)
REVERT: B  232 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6213 (mp0)
REVERT: B  291 LYS cc_start: 0.6107 (mmmt) cc_final: 0.5622 (tptp)
REVERT: B  395 HIS cc_start: 0.7507 (t-170) cc_final: 0.6290 (m90)
REVERT: B  505 TRP cc_start: 0.8273 (m100) cc_final: 0.7868 (m100)
REVERT: B  545 LYS cc_start: 0.7531 (mptt) cc_final: 0.6733 (pttm)
REVERT: B  555 MET cc_start: 0.8433 (mmm) cc_final: 0.8166 (mmp)
  outliers start: 30
  outliers final: 9
  residues processed: 156
  average time/residue: 0.5819
  time to fit residues: 96.2560
Evaluate side-chains
  145 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 GLU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  571 SER
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 39 optimal weight:    0.0270
   chunk 64 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    1.0640

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.180729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.117254 restraints weight = 8432.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.94
r_work: 0.3301 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8587  Z= 0.138
  Angle     :  0.556   6.711  11641  Z= 0.285
  Chirality :  0.041   0.162   1387
  Planarity :  0.004   0.034   1424
  Dihedral  :  4.959  24.380   1188
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 13.02 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.56 (0.25), residues: 1056
  helix: -1.61 (0.20), residues: 616
  sheet: -1.18 (0.56), residues: 76
  loop : -1.63 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 158 
 TYR   0.039   0.002   TYR B 475 
 PHE   0.012   0.001   PHE A 499 
 TRP   0.010   0.001   TRP B 447 
 HIS   0.004   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8587)
  covalent geometry    : angle       0.55610 (11641)
  hydrogen bonds       : bond        0.03177 (  290)
  hydrogen bonds       : angle       4.44045 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.5335 (tt0) cc_final: 0.5086 (tt0)
REVERT: A  176 ASP cc_start: 0.7147 (t0) cc_final: 0.5818 (p0)
REVERT: A  180 ARG cc_start: 0.7011 (mtp180) cc_final: 0.6529 (mtm180)
REVERT: A  232 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6760 (mt-10)
REVERT: A  280 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5689 (mm)
REVERT: A  288 PHE cc_start: 0.6980 (t80) cc_final: 0.6701 (t80)
REVERT: A  291 LYS cc_start: 0.6205 (mmmt) cc_final: 0.5822 (tptp)
REVERT: A  315 PHE cc_start: 0.6977 (t80) cc_final: 0.6757 (t80)
REVERT: A  474 MET cc_start: 0.7782 (ttt) cc_final: 0.7571 (ttt)
REVERT: A  475 TYR cc_start: 0.8237 (p90) cc_final: 0.8015 (p90)
REVERT: A  555 MET cc_start: 0.8371 (mmm) cc_final: 0.8146 (mmp)
REVERT: A  587 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7560 (mmp-170)
REVERT: A  654 TYR cc_start: 0.8063 (t80) cc_final: 0.7826 (t80)
REVERT: A  658 ARG cc_start: 0.7398 (ttt180) cc_final: 0.7136 (mmm160)
REVERT: B  158 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6946 (ttp80)
REVERT: B  180 ARG cc_start: 0.6779 (mtp180) cc_final: 0.6307 (mtm180)
REVERT: B  291 LYS cc_start: 0.5970 (mmmt) cc_final: 0.5474 (tptp)
REVERT: B  387 PHE cc_start: 0.7351 (m-80) cc_final: 0.6899 (m-80)
REVERT: B  395 HIS cc_start: 0.7425 (t-170) cc_final: 0.6187 (m90)
REVERT: B  430 TYR cc_start: 0.7649 (p90) cc_final: 0.7434 (p90)
REVERT: B  545 LYS cc_start: 0.7479 (mptt) cc_final: 0.6608 (pttm)
REVERT: B  555 MET cc_start: 0.8365 (mmm) cc_final: 0.8132 (mmp)
  outliers start: 29
  outliers final: 9
  residues processed: 152
  average time/residue: 0.5801
  time to fit residues: 93.5495
Evaluate side-chains
  137 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  571 SER
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 14 optimal weight:    0.7980
   chunk 103 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.181219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.118196 restraints weight = 8323.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.92
r_work: 0.3304 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8587  Z= 0.121
  Angle     :  0.531   6.795  11641  Z= 0.270
  Chirality :  0.040   0.155   1387
  Planarity :  0.004   0.033   1424
  Dihedral  :  4.630  19.429   1188
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 14.44 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.10 (0.25), residues: 1056
  helix: -1.23 (0.20), residues: 616
  sheet: -1.00 (0.56), residues: 76
  loop : -1.46 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 158 
 TYR   0.036   0.001   TYR B 475 
 PHE   0.022   0.001   PHE B  42 
 TRP   0.010   0.001   TRP B 447 
 HIS   0.003   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8587)
  covalent geometry    : angle       0.53081 (11641)
  hydrogen bonds       : bond        0.02904 (  290)
  hydrogen bonds       : angle       4.21749 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6816 (mmmm)
REVERT: A  158 ARG cc_start: 0.7182 (ttp80) cc_final: 0.6890 (ttp80)
REVERT: A  176 ASP cc_start: 0.7145 (t0) cc_final: 0.5793 (p0)
REVERT: A  180 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6688 (mtm180)
REVERT: A  196 ASN cc_start: 0.8159 (m-40) cc_final: 0.7934 (m-40)
REVERT: A  232 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6715 (mt-10)
REVERT: A  280 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5648 (mm)
REVERT: A  291 LYS cc_start: 0.6131 (mmmt) cc_final: 0.5782 (tptp)
REVERT: A  430 TYR cc_start: 0.7666 (p90) cc_final: 0.7368 (p90)
REVERT: A  475 TYR cc_start: 0.8246 (p90) cc_final: 0.8034 (p90)
REVERT: A  505 TRP cc_start: 0.8250 (m100) cc_final: 0.7741 (m100)
REVERT: A  587 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7551 (mmp-170)
REVERT: A  658 ARG cc_start: 0.7440 (ttt180) cc_final: 0.7133 (mmm160)
REVERT: B  180 ARG cc_start: 0.6939 (mtp180) cc_final: 0.6496 (mtm180)
REVERT: B  188 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7319 (pp20)
REVERT: B  291 LYS cc_start: 0.5946 (mmmt) cc_final: 0.5459 (tptp)
REVERT: B  387 PHE cc_start: 0.7318 (m-80) cc_final: 0.6872 (m-80)
REVERT: B  395 HIS cc_start: 0.7424 (t-170) cc_final: 0.6168 (m90)
REVERT: B  505 TRP cc_start: 0.8255 (m100) cc_final: 0.7717 (m100)
REVERT: B  545 LYS cc_start: 0.7442 (mptt) cc_final: 0.6526 (pttm)
REVERT: B  555 MET cc_start: 0.8323 (mmm) cc_final: 0.7968 (mmm)
  outliers start: 33
  outliers final: 14
  residues processed: 154
  average time/residue: 0.5699
  time to fit residues: 93.3240
Evaluate side-chains
  144 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  571 SER
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 74 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0670
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.2722

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.179933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.128184 restraints weight = 8435.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.90
r_work: 0.3318 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8587  Z= 0.154
  Angle     :  0.565   6.784  11641  Z= 0.285
  Chirality :  0.042   0.152   1387
  Planarity :  0.004   0.044   1424
  Dihedral  :  4.687  24.390   1188
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.55 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.01 (0.25), residues: 1056
  helix: -1.14 (0.20), residues: 618
  sheet: -1.11 (0.55), residues: 80
  loop : -1.43 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 293 
 TYR   0.039   0.002   TYR B 475 
 PHE   0.017   0.002   PHE A 275 
 TRP   0.010   0.002   TRP B 447 
 HIS   0.004   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8587)
  covalent geometry    : angle       0.56466 (11641)
  hydrogen bonds       : bond        0.03154 (  290)
  hydrogen bonds       : angle       4.27586 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.7017 (mmmm)
REVERT: A  180 ARG cc_start: 0.7288 (mtp180) cc_final: 0.6863 (mtm180)
REVERT: A  280 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.5954 (mm)
REVERT: A  291 LYS cc_start: 0.6477 (mmmt) cc_final: 0.6145 (tptp)
REVERT: A  469 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7506 (mt-10)
REVERT: A  658 ARG cc_start: 0.7564 (ttt180) cc_final: 0.7324 (mmm160)
REVERT: B   90 MET cc_start: 0.8318 (tmm) cc_final: 0.7913 (tmt)
REVERT: B  158 ARG cc_start: 0.7308 (ttp80) cc_final: 0.7004 (ttp80)
REVERT: B  180 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6652 (mtm180)
REVERT: B  188 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7497 (pp20)
REVERT: B  287 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5707 (mp)
REVERT: B  291 LYS cc_start: 0.6313 (mmmt) cc_final: 0.5891 (tptp)
REVERT: B  395 HIS cc_start: 0.7540 (t-170) cc_final: 0.6395 (m90)
REVERT: B  545 LYS cc_start: 0.7670 (mptt) cc_final: 0.6766 (pttm)
REVERT: B  555 MET cc_start: 0.8442 (mmm) cc_final: 0.8094 (mmm)
  outliers start: 34
  outliers final: 15
  residues processed: 149
  average time/residue: 0.5305
  time to fit residues: 84.2820
Evaluate side-chains
  142 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  571 SER
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 86 optimal weight:    0.3980
   chunk 70 optimal weight:    8.9990
   chunk 63 optimal weight:    0.2980
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.182689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.119193 restraints weight = 8400.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.95
r_work: 0.3335 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8587  Z= 0.106
  Angle     :  0.534   7.768  11641  Z= 0.269
  Chirality :  0.039   0.146   1387
  Planarity :  0.004   0.064   1424
  Dihedral  :  4.338  20.830   1188
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 15.43 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -1.53 (0.26), residues: 1056
  helix: -0.74 (0.21), residues: 618
  sheet: -0.98 (0.55), residues: 80
  loop : -1.22 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 244 
 TYR   0.035   0.001   TYR A 475 
 PHE   0.021   0.001   PHE B  42 
 TRP   0.010   0.001   TRP B 447 
 HIS   0.003   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8587)
  covalent geometry    : angle       0.53445 (11641)
  hydrogen bonds       : bond        0.02689 (  290)
  hydrogen bonds       : angle       4.01725 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.7077 (mmmm)
REVERT: A  158 ARG cc_start: 0.7142 (ttp80) cc_final: 0.6788 (ttp80)
REVERT: A  180 ARG cc_start: 0.7105 (mtp180) cc_final: 0.6694 (mtm180)
REVERT: A  232 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6492 (mt-10)
REVERT: A  237 LEU cc_start: 0.8166 (mt) cc_final: 0.7744 (tp)
REVERT: A  280 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5836 (mm)
REVERT: A  291 LYS cc_start: 0.6186 (mmmt) cc_final: 0.5853 (tptp)
REVERT: A  489 LEU cc_start: 0.7498 (mp) cc_final: 0.7216 (mt)
REVERT: A  587 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7535 (mmp-170)
REVERT: A  658 ARG cc_start: 0.7320 (ttt180) cc_final: 0.7020 (mmm160)
REVERT: B   90 MET cc_start: 0.8231 (tmm) cc_final: 0.7832 (tmt)
REVERT: B  158 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6727 (ttp80)
REVERT: B  180 ARG cc_start: 0.7069 (mtp180) cc_final: 0.6638 (mtm180)
REVERT: B  196 ASN cc_start: 0.8143 (m-40) cc_final: 0.7928 (m-40)
REVERT: B  232 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6550 (mt-10)
REVERT: B  291 LYS cc_start: 0.6039 (mmmt) cc_final: 0.5643 (tptp)
REVERT: B  395 HIS cc_start: 0.7396 (t-170) cc_final: 0.6156 (m90)
REVERT: B  545 LYS cc_start: 0.7500 (mptt) cc_final: 0.6705 (pttm)
  outliers start: 30
  outliers final: 12
  residues processed: 145
  average time/residue: 0.5282
  time to fit residues: 81.8260
Evaluate side-chains
  140 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0040
   chunk 81 optimal weight:    0.5980
   chunk 86 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    0.3980
   chunk 92 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 58 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.7996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.182592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.119091 restraints weight = 8297.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.94
r_work: 0.3316 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8587  Z= 0.115
  Angle     :  0.539   9.235  11641  Z= 0.270
  Chirality :  0.040   0.148   1387
  Planarity :  0.004   0.049   1424
  Dihedral  :  4.275  23.417   1188
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 15.65 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -1.33 (0.26), residues: 1056
  helix: -0.58 (0.21), residues: 618
  sheet: -0.86 (0.56), residues: 80
  loop : -1.16 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 293 
 TYR   0.038   0.001   TYR A 475 
 PHE   0.014   0.001   PHE B 275 
 TRP   0.010   0.001   TRP B 447 
 HIS   0.003   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8587)
  covalent geometry    : angle       0.53941 (11641)
  hydrogen bonds       : bond        0.02767 (  290)
  hydrogen bonds       : angle       4.00296 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7792 (tmm)
REVERT: A  136 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7116 (mmmm)
REVERT: A  180 ARG cc_start: 0.7110 (mtp180) cc_final: 0.6703 (mtm180)
REVERT: A  232 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6549 (mt-10)
REVERT: A  280 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.5851 (mm)
REVERT: A  283 GLU cc_start: 0.7064 (tp30) cc_final: 0.6836 (mm-30)
REVERT: A  291 LYS cc_start: 0.6168 (mmmt) cc_final: 0.5833 (tptp)
REVERT: A  555 MET cc_start: 0.8218 (mmm) cc_final: 0.7978 (mmm)
REVERT: A  587 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7523 (mmp-170)
REVERT: B   90 MET cc_start: 0.8146 (tmm) cc_final: 0.7630 (tmt)
REVERT: B  158 ARG cc_start: 0.7042 (ttp80) cc_final: 0.6763 (ttp80)
REVERT: B  180 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6636 (mtm180)
REVERT: B  232 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6560 (mt-10)
REVERT: B  291 LYS cc_start: 0.6024 (mmmt) cc_final: 0.5622 (tptp)
REVERT: B  395 HIS cc_start: 0.7409 (t-170) cc_final: 0.6156 (m90)
REVERT: B  430 TYR cc_start: 0.7646 (p90) cc_final: 0.7330 (p90)
REVERT: B  545 LYS cc_start: 0.7513 (mptt) cc_final: 0.6724 (pttm)
  outliers start: 30
  outliers final: 15
  residues processed: 143
  average time/residue: 0.5103
  time to fit residues: 77.9574
Evaluate side-chains
  143 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  569 VAL
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 105 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 78 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 41 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0980
   chunk 77 optimal weight:    0.0030
   chunk 5 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0670
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.2728

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.186653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.127996 restraints weight = 8289.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.22
r_work: 0.3194 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8587  Z= 0.083
  Angle     :  0.512   9.217  11641  Z= 0.253
  Chirality :  0.038   0.145   1387
  Planarity :  0.004   0.050   1424
  Dihedral  :  3.904  14.350   1188
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.74 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.65 (0.27), residues: 1056
  helix: -0.06 (0.22), residues: 610
  sheet: -0.71 (0.57), residues: 80
  loop : -0.76 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 293 
 TYR   0.032   0.001   TYR B 475 
 PHE   0.020   0.001   PHE B  42 
 TRP   0.009   0.001   TRP A 447 
 HIS   0.003   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00185 ( 8587)
  covalent geometry    : angle       0.51220 (11641)
  hydrogen bonds       : bond        0.02423 (  290)
  hydrogen bonds       : angle       3.77776 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.7089 (mmmm)
REVERT: A  180 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6783 (mtm180)
REVERT: A  237 LEU cc_start: 0.8125 (mt) cc_final: 0.7680 (tp)
REVERT: A  276 ASP cc_start: 0.6926 (m-30) cc_final: 0.6621 (m-30)
REVERT: A  280 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5849 (mm)
REVERT: A  430 TYR cc_start: 0.7726 (p90) cc_final: 0.7407 (p90)
REVERT: A  474 MET cc_start: 0.7180 (ttp) cc_final: 0.6747 (ttm)
REVERT: B   90 MET cc_start: 0.8070 (tmm) cc_final: 0.7485 (tmt)
REVERT: B  158 ARG cc_start: 0.7250 (ttp80) cc_final: 0.6938 (ttp80)
REVERT: B  180 ARG cc_start: 0.6952 (mtp180) cc_final: 0.6589 (mtm180)
REVERT: B  291 LYS cc_start: 0.5930 (mmmt) cc_final: 0.5560 (tptp)
REVERT: B  395 HIS cc_start: 0.7405 (t-170) cc_final: 0.6260 (m90)
REVERT: B  430 TYR cc_start: 0.7709 (p90) cc_final: 0.7386 (p90)
REVERT: B  474 MET cc_start: 0.7399 (ttt) cc_final: 0.6958 (ttm)
REVERT: B  545 LYS cc_start: 0.7486 (mptt) cc_final: 0.6762 (pttm)
  outliers start: 23
  outliers final: 7
  residues processed: 148
  average time/residue: 0.4881
  time to fit residues: 77.3808
Evaluate side-chains
  130 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 4 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 49 optimal weight:    0.3980
   chunk 46 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.184681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.128076 restraints weight = 8323.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.00
r_work: 0.3416 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8587  Z= 0.106
  Angle     :  0.557  10.506  11641  Z= 0.276
  Chirality :  0.040   0.145   1387
  Planarity :  0.004   0.034   1424
  Dihedral  :  4.002  15.768   1188
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.38 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.51 (0.27), residues: 1056
  helix:  0.06 (0.22), residues: 614
  sheet: -0.73 (0.57), residues: 80
  loop : -0.69 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 468 
 TYR   0.036   0.001   TYR B 475 
 PHE   0.029   0.001   PHE A 275 
 TRP   0.010   0.001   TRP A 447 
 HIS   0.003   0.001   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8587)
  covalent geometry    : angle       0.55674 (11641)
  hydrogen bonds       : bond        0.02651 (  290)
  hydrogen bonds       : angle       3.84169 (  840)

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

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

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2112 Ramachandran restraints generated.
    1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.7062 (mtp180) cc_final: 0.6765 (mtm180)
REVERT: A  237 LEU cc_start: 0.8288 (mt) cc_final: 0.7869 (tp)
REVERT: A  276 ASP cc_start: 0.7007 (m-30) cc_final: 0.6624 (m-30)
REVERT: A  280 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6005 (mm)
REVERT: A  474 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6869 (ttm)
REVERT: A  489 LEU cc_start: 0.7704 (mp) cc_final: 0.7222 (pp)
REVERT: B   90 MET cc_start: 0.8245 (tmm) cc_final: 0.7656 (tmt)
REVERT: B  158 ARG cc_start: 0.7215 (ttp80) cc_final: 0.6993 (ttp80)
REVERT: B  180 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6844 (mtm180)
REVERT: B  291 LYS cc_start: 0.6179 (mmmt) cc_final: 0.5836 (tptp)
REVERT: B  489 LEU cc_start: 0.7762 (mp) cc_final: 0.7259 (pp)
  outliers start: 18
  outliers final: 10
  residues processed: 132
  average time/residue: 0.5082
  time to fit residues: 71.7028
Evaluate side-chains
  129 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  566 VAL
Chi-restraints excluded: chain B residue  569 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.181681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.128497 restraints weight = 8288.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.03
r_work: 0.3359 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8587  Z= 0.166
  Angle     :  0.623  10.686  11641  Z= 0.305
  Chirality :  0.043   0.143   1387
  Planarity :  0.004   0.035   1424
  Dihedral  :  4.379  28.997   1188
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.71 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.80 (0.26), residues: 1056
  helix: -0.15 (0.21), residues: 612
  sheet: -0.65 (0.57), residues: 78
  loop : -0.92 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 158 
 TYR   0.040   0.002   TYR B 475 
 PHE   0.027   0.002   PHE B 275 
 TRP   0.010   0.002   TRP B 505 
 HIS   0.004   0.001   HIS A 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 8587)
  covalent geometry    : angle       0.62296 (11641)
  hydrogen bonds       : bond        0.03167 (  290)
  hydrogen bonds       : angle       4.12420 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3283.66 seconds
wall clock time: 56 minutes 24.96 seconds (3384.96 seconds total)