Starting phenix.real_space_refine
on Thu Feb 13 01:07:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i39_35146/02_2025/8i39_35146_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i39_35146/02_2025/8i39_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i39_35146/02_2025/8i39_35146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i39_35146/02_2025/8i39_35146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i39_35146/02_2025/8i39_35146_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i39_35146/02_2025/8i39_35146_trim.cif"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.184
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8413
  Number of models: 1
  Model: ""
    Number of chains: 2
    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: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'A8S': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.00, per 1000 atoms: 0.83
  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: 2.07
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.79
  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: 2.48

  Time building geometry restraints manager: 2.35 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:             0.660
  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:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.450
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.160
-------------------------------------------------------------------------------
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= 0.550
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.018   0.003   TRP A 426 
 HIS   0.011   0.003   HIS B 427 
 PHE   0.028   0.002   PHE B 499 
 TYR   0.027   0.003   TYR A 475 
 ARG   0.008   0.001   ARG B  48 

*********************** 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  : 0.864 
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: 0.6310 (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: 0.7924 (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: 1.3395
  time to fit residues: 210.2139
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  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 80 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:   20.0000
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.182641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.133476 restraints weight = 8432.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.09
r_work: 0.3433 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.2061

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= 0.203
  Angle     :  0.622   5.294  11641  Z= 0.322
  Chirality :  0.042   0.143   1387
  Planarity :  0.005   0.038   1424
  Dihedral  :  6.759  44.626   1188
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.47 (0.22), residues: 1056
  helix: -3.28 (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
 TRP   0.011   0.002   TRP A 447 
 HIS   0.005   0.001   HIS B 427 
 PHE   0.021   0.001   PHE A 144 
 TYR   0.021   0.001   TYR B 475 
 ARG   0.007   0.000   ARG B 293 

*********************** 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
  162 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6848 (tmm)
REVERT: A   97 MET cc_start: 0.6651 (ttm) cc_final: 0.6383 (ttm)
REVERT: A  148 ASP cc_start: 0.7780 (m-30) cc_final: 0.7532 (m-30)
REVERT: A  180 ARG cc_start: 0.7014 (mtp180) cc_final: 0.6609 (mtm180)
REVERT: A  232 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7067 (mt-10)
REVERT: A  291 LYS cc_start: 0.6373 (mmmt) cc_final: 0.5005 (ttpp)
REVERT: A  424 MET cc_start: 0.8094 (mmm) cc_final: 0.7880 (mmm)
REVERT: A  430 TYR cc_start: 0.7743 (p90) cc_final: 0.7528 (p90)
REVERT: A  469 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7376 (mt-10)
REVERT: A  474 MET cc_start: 0.7963 (ttt) cc_final: 0.7698 (ttt)
REVERT: A  475 TYR cc_start: 0.8370 (p90) cc_final: 0.7974 (p90)
REVERT: A  555 MET cc_start: 0.8591 (mmm) cc_final: 0.8241 (mmm)
REVERT: A  576 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7669 (ttm)
REVERT: B   97 MET cc_start: 0.6519 (ttm) cc_final: 0.6173 (ttm)
REVERT: B  158 ARG cc_start: 0.7270 (ttp80) cc_final: 0.6903 (ttp80)
REVERT: B  180 ARG cc_start: 0.6914 (mtp180) cc_final: 0.6419 (mtm180)
REVERT: B  291 LYS cc_start: 0.6546 (mmmt) cc_final: 0.6040 (tptp)
REVERT: B  395 HIS cc_start: 0.7491 (t-170) cc_final: 0.6282 (m90)
REVERT: B  430 TYR cc_start: 0.7748 (p90) cc_final: 0.7390 (p90)
REVERT: B  474 MET cc_start: 0.7693 (ttt) cc_final: 0.7463 (ttt)
REVERT: B  545 LYS cc_start: 0.7676 (mptt) cc_final: 0.6814 (pttm)
REVERT: B  555 MET cc_start: 0.8364 (mmm) cc_final: 0.8065 (mmm)
REVERT: B  658 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7348 (mtm180)
  outliers start: 21
  outliers final: 6
  residues processed: 151
  average time/residue: 1.2651
  time to fit residues: 202.9419
Evaluate side-chains
  130 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
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 83 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 26 optimal weight:   20.0000
   chunk 57 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 65 optimal weight:    0.1980
   chunk 84 optimal weight:    0.5980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.179255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.126812 restraints weight = 8489.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.87
r_work: 0.3302 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8587  Z= 0.224
  Angle     :  0.583   6.618  11641  Z= 0.299
  Chirality :  0.041   0.143   1387
  Planarity :  0.004   0.038   1424
  Dihedral  :  5.305  30.914   1188
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 11.16 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.24), residues: 1056
  helix: -2.33 (0.18), residues: 632
  sheet: -1.88 (0.54), residues: 80
  loop : -1.76 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 447 
 HIS   0.004   0.001   HIS B 427 
 PHE   0.020   0.001   PHE B  42 
 TYR   0.036   0.002   TYR B 475 
 ARG   0.007   0.000   ARG B 293 

*********************** 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
  173 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.5535 (tt0) cc_final: 0.5283 (tt0)
REVERT: A   97 MET cc_start: 0.6628 (ttm) cc_final: 0.6355 (ttm)
REVERT: A  148 ASP cc_start: 0.7783 (m-30) cc_final: 0.7545 (m-30)
REVERT: A  158 ARG cc_start: 0.7344 (ttp80) cc_final: 0.7076 (ttp80)
REVERT: A  180 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6634 (mtm180)
REVERT: A  188 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7604 (pp20)
REVERT: A  232 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7131 (mt-10)
REVERT: A  280 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.5813 (mm)
REVERT: A  291 LYS cc_start: 0.6456 (mmmt) cc_final: 0.6022 (tptp)
REVERT: A  430 TYR cc_start: 0.7853 (p90) cc_final: 0.7490 (p90)
REVERT: A  469 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7482 (mt-10)
REVERT: A  474 MET cc_start: 0.8081 (ttt) cc_final: 0.7797 (ttt)
REVERT: A  555 MET cc_start: 0.8527 (mmm) cc_final: 0.8151 (mmm)
REVERT: A  587 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7672 (mmp-170)
REVERT: A  654 TYR cc_start: 0.8215 (t80) cc_final: 0.8001 (t80)
REVERT: A  658 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7330 (mmm160)
REVERT: B   42 PHE cc_start: 0.6076 (p90) cc_final: 0.5815 (p90)
REVERT: B  180 ARG cc_start: 0.7031 (mtp180) cc_final: 0.6537 (mtm180)
REVERT: B  291 LYS cc_start: 0.6227 (mmmt) cc_final: 0.5738 (tptp)
REVERT: B  395 HIS cc_start: 0.7557 (t-170) cc_final: 0.6401 (m90)
REVERT: B  474 MET cc_start: 0.7871 (ttt) cc_final: 0.7630 (ttt)
REVERT: B  475 TYR cc_start: 0.8490 (p90) cc_final: 0.8286 (p90)
REVERT: B  545 LYS cc_start: 0.7687 (mptt) cc_final: 0.6842 (pttm)
REVERT: B  555 MET cc_start: 0.8490 (mmm) cc_final: 0.8221 (mmp)
  outliers start: 33
  outliers final: 11
  residues processed: 162
  average time/residue: 1.2370
  time to fit residues: 213.3039
Evaluate side-chains
  145 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 GLU
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  444 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  186 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0000
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   chunk 21 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.6584

-------------------------------------------------------------------------------
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 = 0.4095 r_free = 0.4095 target = 0.182462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.128603 restraints weight = 8305.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.75
r_work: 0.3389 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2973

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= 0.157
  Angle     :  0.530   6.606  11641  Z= 0.270
  Chirality :  0.040   0.166   1387
  Planarity :  0.004   0.036   1424
  Dihedral  :  4.813  23.555   1188
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.46 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.25), residues: 1056
  helix: -1.52 (0.20), residues: 616
  sheet: -1.27 (0.55), residues: 76
  loop : -1.62 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 447 
 HIS   0.003   0.001   HIS A 434 
 PHE   0.017   0.001   PHE B  42 
 TYR   0.031   0.001   TYR A 475 
 ARG   0.006   0.000   ARG B 158 

*********************** 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
  161 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.5533 (tt0) cc_final: 0.5311 (tt0)
REVERT: A  148 ASP cc_start: 0.7854 (m-30) cc_final: 0.7617 (m-30)
REVERT: A  180 ARG cc_start: 0.7318 (mtp180) cc_final: 0.6895 (mtm180)
REVERT: A  280 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.5850 (mm)
REVERT: A  288 PHE cc_start: 0.7099 (t80) cc_final: 0.6879 (t80)
REVERT: A  291 LYS cc_start: 0.6458 (mmmt) cc_final: 0.6055 (tptp)
REVERT: A  315 PHE cc_start: 0.7135 (t80) cc_final: 0.6854 (t80)
REVERT: A  430 TYR cc_start: 0.7838 (p90) cc_final: 0.7499 (p90)
REVERT: A  505 TRP cc_start: 0.8263 (m100) cc_final: 0.7879 (m100)
REVERT: A  555 MET cc_start: 0.8505 (mmm) cc_final: 0.8276 (mmp)
REVERT: A  576 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7652 (ttt)
REVERT: A  587 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7604 (mmp-170)
REVERT: A  658 ARG cc_start: 0.7575 (ttt180) cc_final: 0.7327 (mmm160)
REVERT: B  136 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7096 (mmmm)
REVERT: B  158 ARG cc_start: 0.7366 (ttp80) cc_final: 0.7156 (ttp80)
REVERT: B  180 ARG cc_start: 0.7129 (mtp180) cc_final: 0.6688 (mtm180)
REVERT: B  291 LYS cc_start: 0.6254 (mmmt) cc_final: 0.5756 (tptp)
REVERT: B  387 PHE cc_start: 0.7577 (m-80) cc_final: 0.7159 (m-80)
REVERT: B  395 HIS cc_start: 0.7602 (t-170) cc_final: 0.6427 (m90)
REVERT: B  505 TRP cc_start: 0.8265 (m100) cc_final: 0.7856 (m100)
REVERT: B  545 LYS cc_start: 0.7667 (mptt) cc_final: 0.6839 (pttm)
REVERT: B  555 MET cc_start: 0.8457 (mmm) cc_final: 0.8191 (mmp)
  outliers start: 27
  outliers final: 7
  residues processed: 150
  average time/residue: 1.2189
  time to fit residues: 194.8374
Evaluate side-chains
  135 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
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  479 SER
Chi-restraints excluded: chain A residue  571 SER
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  397 LEU
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 25 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.178387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.113608 restraints weight = 8320.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.98
r_work: 0.3241 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8587  Z= 0.305
  Angle     :  0.608   7.242  11641  Z= 0.309
  Chirality :  0.044   0.158   1387
  Planarity :  0.004   0.035   1424
  Dihedral  :  5.074  30.035   1188
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 13.79 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.25), residues: 1056
  helix: -1.51 (0.19), residues: 620
  sheet: -1.10 (0.56), residues: 76
  loop : -1.68 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 426 
 HIS   0.005   0.001   HIS A 434 
 PHE   0.025   0.002   PHE B  42 
 TYR   0.045   0.002   TYR B 475 
 ARG   0.007   0.001   ARG A 158 

*********************** 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
  160 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.5313 (tt0) cc_final: 0.5091 (tt0)
REVERT: A  136 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6798 (mmmm)
REVERT: A  148 ASP cc_start: 0.7543 (m-30) cc_final: 0.7334 (m-30)
REVERT: A  158 ARG cc_start: 0.7059 (ttp80) cc_final: 0.6832 (ttp80)
REVERT: A  180 ARG cc_start: 0.6970 (mtp180) cc_final: 0.6496 (mtm180)
REVERT: A  280 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.5775 (mm)
REVERT: A  288 PHE cc_start: 0.6922 (t80) cc_final: 0.6629 (t80)
REVERT: A  291 LYS cc_start: 0.6158 (mmmt) cc_final: 0.5804 (tptp)
REVERT: A  576 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7834 (ttt)
REVERT: A  658 ARG cc_start: 0.7467 (ttt180) cc_final: 0.7159 (mmm160)
REVERT: B   42 PHE cc_start: 0.6234 (p90) cc_final: 0.6001 (p90)
REVERT: B  180 ARG cc_start: 0.6756 (mtp180) cc_final: 0.6240 (mtm180)
REVERT: B  188 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7377 (pp20)
REVERT: B  291 LYS cc_start: 0.6118 (mmmt) cc_final: 0.5641 (tptp)
REVERT: B  395 HIS cc_start: 0.7501 (t-170) cc_final: 0.6351 (m90)
REVERT: B  430 TYR cc_start: 0.7730 (p90) cc_final: 0.7189 (p90)
REVERT: B  545 LYS cc_start: 0.7485 (mptt) cc_final: 0.6535 (pttm)
REVERT: B  555 MET cc_start: 0.8344 (mmm) cc_final: 0.8134 (mmp)
  outliers start: 39
  outliers final: 17
  residues processed: 150
  average time/residue: 1.1825
  time to fit residues: 189.4504
Evaluate side-chains
  142 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
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  186 ILE
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  444 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 A residue  576 MET
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  397 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.4079 r_free = 0.4079 target = 0.181024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.119204 restraints weight = 8348.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.77
r_work: 0.3366 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8587  Z= 0.173
  Angle     :  0.535   6.601  11641  Z= 0.272
  Chirality :  0.040   0.150   1387
  Planarity :  0.004   0.060   1424
  Dihedral  :  4.578  23.063   1188
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 14.22 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.25), residues: 1056
  helix: -1.11 (0.20), residues: 616
  sheet: -0.88 (0.56), residues: 76
  loop : -1.37 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 447 
 HIS   0.003   0.001   HIS A 434 
 PHE   0.023   0.001   PHE B  42 
 TYR   0.035   0.001   TYR A 475 
 ARG   0.017   0.001   ARG B 244 

*********************** 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
  164 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6974 (mmmm)
REVERT: A  158 ARG cc_start: 0.7158 (ttp80) cc_final: 0.6900 (ttp80)
REVERT: A  180 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6767 (mtm180)
REVERT: A  232 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6757 (mt-10)
REVERT: A  280 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.5953 (mm)
REVERT: A  288 PHE cc_start: 0.6952 (t80) cc_final: 0.6584 (t80)
REVERT: A  291 LYS cc_start: 0.6337 (mmmt) cc_final: 0.6007 (tptp)
REVERT: A  315 PHE cc_start: 0.7250 (t80) cc_final: 0.7048 (t80)
REVERT: A  505 TRP cc_start: 0.8265 (m100) cc_final: 0.7870 (m100)
REVERT: A  555 MET cc_start: 0.8417 (mmm) cc_final: 0.8127 (mmm)
REVERT: A  576 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7659 (ttt)
REVERT: B  136 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7094 (mmmm)
REVERT: B  158 ARG cc_start: 0.7224 (ttp80) cc_final: 0.6909 (ttp80)
REVERT: B  180 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6616 (mtm180)
REVERT: B  188 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7449 (pp20)
REVERT: B  232 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6623 (mt-10)
REVERT: B  291 LYS cc_start: 0.6143 (mmmt) cc_final: 0.5684 (tptp)
REVERT: B  387 PHE cc_start: 0.7486 (m-80) cc_final: 0.7072 (m-80)
REVERT: B  395 HIS cc_start: 0.7515 (t-170) cc_final: 0.6362 (m90)
REVERT: B  430 TYR cc_start: 0.7835 (p90) cc_final: 0.7313 (p90)
REVERT: B  505 TRP cc_start: 0.8258 (m100) cc_final: 0.7863 (m100)
REVERT: B  545 LYS cc_start: 0.7554 (mptt) cc_final: 0.6714 (pttm)
REVERT: B  555 MET cc_start: 0.8411 (mmm) cc_final: 0.8201 (mmp)
  outliers start: 36
  outliers final: 16
  residues processed: 154
  average time/residue: 1.1701
  time to fit residues: 192.3376
Evaluate side-chains
  145 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  444 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  569 VAL
Chi-restraints excluded: chain A residue  571 SER
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  397 LEU
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  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 28 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 88 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.181863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.118523 restraints weight = 8336.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.93
r_work: 0.3328 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.3397

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= 0.171
  Angle     :  0.539   8.436  11641  Z= 0.271
  Chirality :  0.040   0.147   1387
  Planarity :  0.004   0.046   1424
  Dihedral  :  4.398  21.865   1188
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 14.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.26), residues: 1056
  helix: -0.78 (0.21), residues: 616
  sheet: -0.55 (0.59), residues: 66
  loop : -1.28 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 447 
 HIS   0.003   0.001   HIS A 434 
 PHE   0.011   0.001   PHE A 499 
 TYR   0.037   0.001   TYR B 475 
 ARG   0.012   0.000   ARG B 293 

*********************** 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
  162 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 121
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7668 (tmm)
REVERT: A  136 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7065 (mmmm)
REVERT: A  180 ARG cc_start: 0.7141 (mtp180) cc_final: 0.6728 (mtm180)
REVERT: A  232 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6638 (mt-10)
REVERT: A  280 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5871 (mm)
REVERT: A  291 LYS cc_start: 0.6143 (mmmt) cc_final: 0.5807 (tptp)
REVERT: A  474 MET cc_start: 0.7111 (ttp) cc_final: 0.6834 (ttm)
REVERT: A  505 TRP cc_start: 0.8247 (m100) cc_final: 0.7777 (m100)
REVERT: A  555 MET cc_start: 0.8302 (mmm) cc_final: 0.8027 (mmm)
REVERT: A  576 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7644 (ttt)
REVERT: A  587 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7535 (mmp-170)
REVERT: B   90 MET cc_start: 0.8151 (tmm) cc_final: 0.7864 (tmt)
REVERT: B  136 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7063 (mmmm)
REVERT: B  158 ARG cc_start: 0.7046 (ttp80) cc_final: 0.6780 (ttp80)
REVERT: B  180 ARG cc_start: 0.7081 (mtp180) cc_final: 0.6656 (mtm180)
REVERT: B  188 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7268 (pp20)
REVERT: B  232 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6516 (mt-10)
REVERT: B  291 LYS cc_start: 0.6005 (mmmt) cc_final: 0.5597 (tptp)
REVERT: B  395 HIS cc_start: 0.7356 (t-170) cc_final: 0.6191 (m90)
REVERT: B  474 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6873 (ttm)
REVERT: B  505 TRP cc_start: 0.8251 (m100) cc_final: 0.7841 (m100)
REVERT: B  545 LYS cc_start: 0.7401 (mptt) cc_final: 0.6543 (pttm)
REVERT: B  603 MET cc_start: 0.6904 (mtp) cc_final: 0.6591 (ptp)
  outliers start: 41
  outliers final: 18
  residues processed: 149
  average time/residue: 1.1331
  time to fit residues: 180.4035
Evaluate side-chains
  146 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
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  571 SER
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  232 GLU
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  450 LEU
Chi-restraints excluded: chain B residue  474 MET
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 90 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0670
   chunk 35 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 74 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.4122

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.178974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.114959 restraints weight = 8315.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 1.90
r_work: 0.3080 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.3347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8587  Z= 0.257
  Angle     :  0.589   8.683  11641  Z= 0.292
  Chirality :  0.043   0.149   1387
  Planarity :  0.004   0.050   1424
  Dihedral  :  4.628  34.891   1188
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 15.43 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.25), residues: 1056
  helix: -0.85 (0.20), residues: 620
  sheet: -0.49 (0.59), residues: 66
  loop : -1.30 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 426 
 HIS   0.004   0.001   HIS A 434 
 PHE   0.022   0.002   PHE A 275 
 TYR   0.041   0.002   TYR A 475 
 ARG   0.013   0.001   ARG B 293 

*********************** 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
  151 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.7010 (mmmm)
REVERT: A  158 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6857 (ttp80)
REVERT: A  180 ARG cc_start: 0.7175 (mtp180) cc_final: 0.6763 (mtm180)
REVERT: A  232 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6800 (mt-10)
REVERT: A  280 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.5947 (mm)
REVERT: A  291 LYS cc_start: 0.6112 (mmmt) cc_final: 0.5787 (tptp)
REVERT: A  555 MET cc_start: 0.8376 (mmm) cc_final: 0.8095 (mmm)
REVERT: A  576 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7863 (ttt)
REVERT: A  587 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7717 (mmp-170)
REVERT: B   90 MET cc_start: 0.8192 (tmm) cc_final: 0.7628 (tmt)
REVERT: B  136 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6988 (mmmm)
REVERT: B  180 ARG cc_start: 0.7028 (mtp180) cc_final: 0.6523 (mtm180)
REVERT: B  291 LYS cc_start: 0.6075 (mmmt) cc_final: 0.5671 (tptp)
REVERT: B  395 HIS cc_start: 0.7502 (t-170) cc_final: 0.6315 (m90)
REVERT: B  545 LYS cc_start: 0.7538 (mptt) cc_final: 0.6648 (pttm)
  outliers start: 36
  outliers final: 15
  residues processed: 138
  average time/residue: 1.2073
  time to fit residues: 177.7490
Evaluate side-chains
  132 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
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  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  571 SER
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  268 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0770
   chunk 50 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    0.7138

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.181527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.117863 restraints weight = 8324.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.90
r_work: 0.3237 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8587  Z= 0.163
  Angle     :  0.551   9.105  11641  Z= 0.271
  Chirality :  0.040   0.146   1387
  Planarity :  0.004   0.047   1424
  Dihedral  :  4.315  29.235   1188
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.19 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.26), residues: 1056
  helix: -0.43 (0.21), residues: 604
  sheet: -0.43 (0.61), residues: 66
  loop : -0.99 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 447 
 HIS   0.003   0.001   HIS A 434 
 PHE   0.024   0.001   PHE B  42 
 TYR   0.036   0.001   TYR A 475 
 ARG   0.012   0.001   ARG B 293 

*********************** 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
  148 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7107 (mmmm)
REVERT: A  158 ARG cc_start: 0.7092 (ttp80) cc_final: 0.6731 (ttp80)
REVERT: A  180 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6715 (mtm180)
REVERT: A  196 ASN cc_start: 0.8134 (m-40) cc_final: 0.7925 (m-40)
REVERT: A  232 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6835 (mt-10)
REVERT: A  280 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5860 (mm)
REVERT: A  474 MET cc_start: 0.7219 (ttp) cc_final: 0.6824 (ttm)
REVERT: A  555 MET cc_start: 0.8345 (mmm) cc_final: 0.8065 (mmm)
REVERT: A  576 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7661 (ttt)
REVERT: A  587 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7601 (mmp-170)
REVERT: B   90 MET cc_start: 0.8178 (tmm) cc_final: 0.7844 (tmt)
REVERT: B  136 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7141 (mmmm)
REVERT: B  158 ARG cc_start: 0.7086 (ttp80) cc_final: 0.6741 (ttp80)
REVERT: B  180 ARG cc_start: 0.7112 (mtp180) cc_final: 0.6675 (mtm180)
REVERT: B  232 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6646 (mt-10)
REVERT: B  291 LYS cc_start: 0.6016 (mmmt) cc_final: 0.5609 (tptp)
REVERT: B  395 HIS cc_start: 0.7356 (t-170) cc_final: 0.6197 (m90)
REVERT: B  545 LYS cc_start: 0.7529 (mptt) cc_final: 0.6771 (pttm)
  outliers start: 31
  outliers final: 16
  residues processed: 139
  average time/residue: 1.1900
  time to fit residues: 176.8740
Evaluate side-chains
  138 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
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  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  571 SER
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  232 GLU
Chi-restraints excluded: chain B residue  388 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 87 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 105 optimal weight:    0.2980
   chunk 66 optimal weight:    0.0670
   chunk 46 optimal weight:    0.0050
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.4132

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.185216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.129190 restraints weight = 8249.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.86
r_work: 0.3424 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.3776

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= 0.130
  Angle     :  0.531   9.710  11641  Z= 0.262
  Chirality :  0.039   0.145   1387
  Planarity :  0.004   0.053   1424
  Dihedral  :  4.021  17.771   1188
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 18.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.26), residues: 1056
  helix: -0.04 (0.22), residues: 606
  sheet: -0.51 (0.57), residues: 76
  loop : -0.86 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 447 
 HIS   0.003   0.001   HIS A 434 
 PHE   0.026   0.001   PHE A 275 
 TYR   0.033   0.001   TYR B 475 
 ARG   0.013   0.001   ARG B 293 

********************** 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: 13
    poor density    : 125
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8174 (tmm) cc_final: 0.7819 (tmt)
REVERT: A  158 ARG cc_start: 0.7272 (ttp80) cc_final: 0.6983 (ttp80)
REVERT: A  180 ARG cc_start: 0.7082 (mtp180) cc_final: 0.6787 (mtm180)
REVERT: A  232 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6866 (mt-10)
REVERT: A  237 LEU cc_start: 0.8364 (mt) cc_final: 0.8024 (tp)
REVERT: A  280 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6037 (mm)
REVERT: A  474 MET cc_start: 0.7226 (ttp) cc_final: 0.6784 (ttm)
REVERT: A  542 MET cc_start: 0.7670 (mmt) cc_final: 0.7377 (mmm)
REVERT: A  576 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7676 (ttt)
REVERT: A  587 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7624 (mmp-170)
REVERT: B  136 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7204 (mmmm)
REVERT: B  158 ARG cc_start: 0.7316 (ttp80) cc_final: 0.7087 (ttp80)
REVERT: B  180 ARG cc_start: 0.7259 (mtp180) cc_final: 0.6876 (mtm180)
REVERT: B  291 LYS cc_start: 0.6196 (mmmt) cc_final: 0.5803 (tptp)
REVERT: B  395 HIS cc_start: 0.7536 (t-170) cc_final: 0.6360 (m90)
REVERT: B  474 MET cc_start: 0.7237 (ttp) cc_final: 0.6793 (ttm)
REVERT: B  545 LYS cc_start: 0.7610 (mptt) cc_final: 0.6919 (pttm)
REVERT: B  603 MET cc_start: 0.6815 (mtp) cc_final: 0.6590 (ptp)
  outliers start: 13
  outliers final: 5
  residues processed: 134
  average time/residue: 1.1377
  time to fit residues: 163.3275
Evaluate side-chains
  122 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 112
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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  576 MET
Chi-restraints excluded: chain A residue  587 ARG
Chi-restraints excluded: chain B residue  136 LYS
Chi-restraints excluded: chain B residue  388 SER
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 74 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 90 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 93 optimal weight:    0.4980
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 63 optimal weight:    0.4980
   chunk 105 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4116 r_free = 0.4116 target = 0.184925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.128520 restraints weight = 8375.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.89
r_work: 0.3401 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8587  Z= 0.153
  Angle     :  0.531  10.782  11641  Z= 0.265
  Chirality :  0.040   0.145   1387
  Planarity :  0.004   0.033   1424
  Dihedral  :  4.016  17.076   1188
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.04 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.27), residues: 1056
  helix:  0.07 (0.22), residues: 608
  sheet: -0.47 (0.58), residues: 76
  loop : -0.79 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 447 
 HIS   0.003   0.001   HIS A 434 
 PHE   0.032   0.001   PHE A 275 
 TYR   0.034   0.001   TYR A 475 
 ARG   0.007   0.000   ARG B 158 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6665.39 seconds
wall clock time: 117 minutes 58.08 seconds (7078.08 seconds total)