Starting phenix.real_space_refine
on Sun Aug 24 13:27:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jgs_36245/08_2025/8jgs_36245.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jgs_36245/08_2025/8jgs_36245.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jgs_36245/08_2025/8jgs_36245.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jgs_36245/08_2025/8jgs_36245.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jgs_36245/08_2025/8jgs_36245.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jgs_36245/08_2025/8jgs_36245.map"
  }
  resolution = 3.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    6630      2.51       5
     N    1650      2.21       5
     O    1740      1.98       5
     H   10182      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20268
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 639, 10134
          Classifications: {'peptide': 639}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 10134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 639, 10134
          Classifications: {'peptide': 639}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613}
          Chain breaks: 6
  Time building chain proxies: 4.48, per 1000 atoms: 0.22
  Number of scatterers: 20268
  At special positions: 0
  Unit cell: (97.65, 99.51, 100.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      66     16.00
     O    1740      8.00
     N    1650      7.00
     C    6630      6.00
     H   10182      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 399 " - pdb=" SG  CYS A 408 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 498 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  97 " - pdb=" SG  CYS B 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 399 " - pdb=" SG  CYS B 408 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 498 " - pdb=" SG  CYS B 504 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 669.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 6 sheets defined
      69.6% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 48
      removed outlier: 3.751A  pdb=" N   LYS A  48 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 91
      removed outlier: 3.679A  pdb=" N   MET A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLY A  64 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   TRP A  65 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP A  91 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 111
    Processing helix  chain 'A' and resid 129 through 134
    Processing helix  chain 'A' and resid 143 through 169
    Processing helix  chain 'A' and resid 176 through 185
    Processing helix  chain 'A' and resid 189 through 193
      removed outlier: 4.048A  pdb=" N   LEU A 193 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 211
    Processing helix  chain 'A' and resid 220 through 235
      removed outlier: 4.040A  pdb=" N   LEU A 235 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 241
    Processing helix  chain 'A' and resid 242 through 263
      removed outlier: 3.541A  pdb=" N   LYS A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   ALA A 255 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ALA A 256 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 257 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   PHE A 262 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 275
    Processing helix  chain 'A' and resid 282 through 302
      removed outlier: 4.014A  pdb=" N   TRP A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ARG A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A 291 " --> pdb=" O   ARG A 287 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA A 292 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 325 through 332
      removed outlier: 4.011A  pdb=" N   PHE A 329 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 356
      removed outlier: 3.754A  pdb=" N   ARG A 345 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ILE A 348 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 3.514A  pdb=" N   GLY A 360 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 379
      removed outlier: 3.558A  pdb=" N   ALA A 378 " --> pdb=" O   THR A 374 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   PHE A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 386
    Processing helix  chain 'A' and resid 388 through 397
    Processing helix  chain 'A' and resid 433 through 452
      removed outlier: 3.836A  pdb=" N   PHE A 452 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 489
      removed outlier: 3.656A  pdb=" N   VAL A 477 " --> pdb=" O   ALA A 473 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   TYR A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 496
      removed outlier: 3.592A  pdb=" N   GLU A 496 " --> pdb=" O   PHE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 524
      removed outlier: 3.565A  pdb=" N   TYR A 510 " --> pdb=" O   THR A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 537
      removed outlier: 3.618A  pdb=" N   THR A 537 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 558
      removed outlier: 4.338A  pdb=" N   LEU A 546 " --> pdb=" O   TYR A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 572
    Processing helix  chain 'A' and resid 589 through 594
      removed outlier: 4.200A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 623
    Processing helix  chain 'A' and resid 645 through 659
    Processing helix  chain 'A' and resid 703 through 714
      removed outlier: 4.316A  pdb=" N   ASP A 709 " --> pdb=" O   GLU A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 741
    Processing helix  chain 'B' and resid 28 through 47
    Processing helix  chain 'B' and resid 50 through 91
      removed outlier: 3.838A  pdb=" N   MET B  54 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TRP B  65 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   VAL B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASP B  91 " --> pdb=" O   ASP B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 111
    Processing helix  chain 'B' and resid 129 through 134
    Processing helix  chain 'B' and resid 143 through 169
    Processing helix  chain 'B' and resid 176 through 185
    Processing helix  chain 'B' and resid 189 through 193
      removed outlier: 4.067A  pdb=" N   LEU B 193 " --> pdb=" O   ARG B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 211
    Processing helix  chain 'B' and resid 220 through 235
      removed outlier: 3.588A  pdb=" N   SER B 233 " --> pdb=" O   GLY B 229 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LEU B 235 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 241
    Processing helix  chain 'B' and resid 242 through 261
      removed outlier: 4.554A  pdb=" N   ALA B 255 " --> pdb=" O   SER B 251 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ALA B 256 " --> pdb=" O   ALA B 252 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLY B 257 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 275
    Processing helix  chain 'B' and resid 281 through 302
      removed outlier: 3.764A  pdb=" N   LEU B 285 " --> pdb=" O   PRO B 281 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   TRP B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ARG B 287 " --> pdb=" O   LYS B 283 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA B 291 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA B 292 " --> pdb=" O   SER B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 324
      No H-bonds generated for 'chain 'B' and resid 322 through 324'
    Processing helix  chain 'B' and resid 325 through 332
      removed outlier: 3.968A  pdb=" N   PHE B 329 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 356
      removed outlier: 3.910A  pdb=" N   ARG B 345 " --> pdb=" O   ALA B 341 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE B 348 " --> pdb=" O   ILE B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 361
    Processing helix  chain 'B' and resid 362 through 379
      removed outlier: 3.820A  pdb=" N   PHE B 379 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 386
    Processing helix  chain 'B' and resid 388 through 397
    Processing helix  chain 'B' and resid 433 through 452
    Processing helix  chain 'B' and resid 462 through 489
      removed outlier: 3.747A  pdb=" N   VAL B 477 " --> pdb=" O   ALA B 473 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   TYR B 487 " --> pdb=" O   GLN B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 496
    Processing helix  chain 'B' and resid 506 through 524
      removed outlier: 3.565A  pdb=" N   TYR B 510 " --> pdb=" O   THR B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 537
      removed outlier: 3.627A  pdb=" N   THR B 537 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 559
      removed outlier: 4.216A  pdb=" N   LEU B 546 " --> pdb=" O   TYR B 542 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA B 559 " --> pdb=" O   TRP B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 572
    Processing helix  chain 'B' and resid 616 through 623
    Processing helix  chain 'B' and resid 645 through 659
    Processing helix  chain 'B' and resid 703 through 714
      removed outlier: 3.552A  pdb=" N   VAL B 707 " --> pdb=" O   PRO B 703 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ASP B 709 " --> pdb=" O   GLU B 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 733 through 741
    Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 97
      removed outlier: 3.898A  pdb=" N   ILE A  96 " --> pdb=" O   LYS A 127 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LYS A 127 " --> pdb=" O   ILE A  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 627 through 628
      removed outlier: 3.692A  pdb=" N   PHE A 628 " --> pdb=" O   ALA A 643 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 697 through 699
      removed outlier: 6.038A  pdb=" N   VAL A 698 " --> pdb=" O   THR A 722 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   CYS A 719 " --> pdb=" O   ILE A 730 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ILE A 730 " --> pdb=" O   CYS A 719 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL A 721 " --> pdb=" O   LEU A 728 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 95 through 97
      removed outlier: 3.791A  pdb=" N   ILE B  96 " --> pdb=" O   LYS B 127 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LYS B 127 " --> pdb=" O   ILE B  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 627 through 628
      removed outlier: 3.674A  pdb=" N   PHE B 628 " --> pdb=" O   ALA B 643 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA B 643 " --> pdb=" O   PHE B 628 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 697 through 699
      removed outlier: 6.132A  pdb=" N   VAL B 698 " --> pdb=" O   THR B 722 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   CYS B 719 " --> pdb=" O   ILE B 730 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ILE B 730 " --> pdb=" O   CYS B 719 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   VAL B 721 " --> pdb=" O   LEU B 728 " (cutoff:3.500A)

    590 hydrogen bonds defined for protein.
    1746 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: 4.75

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10160
        1.03 -     1.23: 42
        1.23 -     1.43: 4378
        1.43 -     1.62: 5856
        1.62 -     1.82: 98
  Bond restraints: 20534
  Sorted by residual:
  bond pdb=" CB  TRP A 153 "
       pdb=" CG  TRP A 153 "
    ideal  model  delta    sigma   weight residual
    1.498  1.534 -0.036 3.10e-02 1.04e+03 1.39e+00
  bond pdb=" CE3 TRP A 153 "
       pdb=" HE3 TRP A 153 "
    ideal  model  delta    sigma   weight residual
    0.930  0.908  0.022 2.00e-02 2.50e+03 1.16e+00
  bond pdb=" C   THR A 319 "
       pdb=" N   PRO A 320 "
    ideal  model  delta    sigma   weight residual
    1.331  1.344 -0.012 1.21e-02 6.83e+03 1.05e+00
  bond pdb=" CG  TRP A 153 "
       pdb=" CD2 TRP A 153 "
    ideal  model  delta    sigma   weight residual
    1.433  1.451 -0.018 1.80e-02 3.09e+03 1.00e+00
  bond pdb=" CB  TRP B 153 "
       pdb=" CG  TRP B 153 "
    ideal  model  delta    sigma   weight residual
    1.498  1.528 -0.030 3.10e-02 1.04e+03 9.36e-01
  ... (remaining 20529 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 33898
        1.00 -     2.01: 2956
        2.01 -     3.01: 190
        3.01 -     4.01: 53
        4.01 -     5.01: 13
  Bond angle restraints: 37110
  Sorted by residual:
  angle pdb=" N   GLY B 267 "
        pdb=" CA  GLY B 267 "
        pdb=" C   GLY B 267 "
      ideal   model   delta    sigma   weight residual
     112.73  108.68    4.05 1.20e+00 6.94e-01 1.14e+01
  angle pdb=" CB  TRP A 153 "
        pdb=" CG  TRP A 153 "
        pdb=" CD2 TRP A 153 "
      ideal   model   delta    sigma   weight residual
     126.80  130.73   -3.93 1.40e+00 5.10e-01 7.88e+00
  angle pdb=" C   TRP B 286 "
        pdb=" CA  TRP B 286 "
        pdb=" CB  TRP B 286 "
      ideal   model   delta    sigma   weight residual
     110.88  114.60   -3.72 1.57e+00 4.06e-01 5.61e+00
  angle pdb=" CB  TRP A 153 "
        pdb=" CG  TRP A 153 "
        pdb=" CD1 TRP A 153 "
      ideal   model   delta    sigma   weight residual
     126.90  123.37    3.53 1.50e+00 4.44e-01 5.53e+00
  angle pdb=" N   GLU A 541 "
        pdb=" CA  GLU A 541 "
        pdb=" C   GLU A 541 "
      ideal   model   delta    sigma   weight residual
     113.61  110.21    3.40 1.50e+00 4.44e-01 5.14e+00
  ... (remaining 37105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 8678
       17.98 -    35.96: 721
       35.96 -    53.93: 171
       53.93 -    71.91: 74
       71.91 -    89.89: 14
  Dihedral angle restraints: 9658
    sinusoidal: 5080
      harmonic: 4578
  Sorted by residual:
  dihedral pdb=" CA  GLU A 274 "
           pdb=" C   GLU A 274 "
           pdb=" N   GLU A 275 "
           pdb=" CA  GLU A 275 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  GLU B 274 "
           pdb=" C   GLU B 274 "
           pdb=" N   GLU B 275 "
           pdb=" CA  GLU B 275 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  LEU B 540 "
           pdb=" C   LEU B 540 "
           pdb=" N   GLU B 541 "
           pdb=" CA  GLU B 541 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.15   21.85     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 9655 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1331
       0.050 -    0.099: 216
       0.099 -    0.148: 36
       0.148 -    0.198: 1
       0.198 -    0.247: 2
  Chirality restraints: 1586
  Sorted by residual:
  chirality pdb=" CA  TRP A 153 "
            pdb=" N   TRP A 153 "
            pdb=" C   TRP A 153 "
            pdb=" CB  TRP A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  TRP B 153 "
            pdb=" N   TRP B 153 "
            pdb=" C   TRP B 153 "
            pdb=" CB  TRP B 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  VAL A 458 "
            pdb=" N   VAL A 458 "
            pdb=" C   VAL A 458 "
            pdb=" CB  VAL A 458 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 1583 not shown)

  Planarity restraints: 2932
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 286 "   -0.029 2.00e-02 2.50e+03   1.95e-02 1.51e+01
        pdb=" CG  TRP B 286 "    0.068 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 286 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 286 "    0.006 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 286 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 286 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 286 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 286 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 286 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 286 "   -0.003 2.00e-02 2.50e+03
        pdb=" HD1 TRP B 286 "   -0.012 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 286 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE3 TRP B 286 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B 286 "   -0.000 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B 286 "   -0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP B 286 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 153 "    0.016 2.00e-02 2.50e+03   1.44e-02 8.29e+00
        pdb=" CG  TRP A 153 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 153 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 153 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 153 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 153 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 153 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 153 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 153 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 153 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 153 "    0.008 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 153 "    0.003 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 153 "    0.004 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 153 "   -0.000 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 153 "    0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 153 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 157 "    0.013 2.00e-02 2.50e+03   1.20e-02 4.33e+00
        pdb=" CG  PHE A 157 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 157 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 157 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 157 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 157 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 157 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 157 "   -0.004 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 157 "    0.002 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 157 "    0.003 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 157 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 157 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2929 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 1378
        2.19 -     2.80: 42512
        2.80 -     3.40: 56531
        3.40 -     4.00: 69336
        4.00 -     4.60: 108710
  Nonbonded interactions: 278467
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 219 "
            pdb=" H   VAL A 222 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" O   MET A 449 "
            pdb=" HG1 THR A 453 "
     model   vdw
     1.597 2.450
  nonbonded pdb=" O   HIS B  25 "
            pdb=" H   ILE B 188 "
     model   vdw
     1.609 2.450
  nonbonded pdb=" H   TYR A 322 "
            pdb=" OE2 GLU A 325 "
     model   vdw
     1.626 2.450
  nonbonded pdb=" O   MET B 449 "
            pdb=" HG1 THR B 453 "
     model   vdw
     1.637 2.450
  ... (remaining 278462 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:             0.130
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     21.180
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4504
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      :  0.003   0.036  10358  Z= 0.148
  Angle     :  0.568   5.013  14062  Z= 0.334
  Chirality :  0.038   0.247   1586
  Planarity :  0.005   0.074   1718
  Dihedral  : 13.467  89.890   3632
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 15.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.24), residues: 1250
  helix:  0.02 (0.18), residues: 780
  sheet:  1.16 (1.20), residues: 20
  loop : -1.01 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 247 
 TYR   0.019   0.001   TYR B  59 
 PHE   0.035   0.002   PHE A 157 
 TRP   0.065   0.002   TRP B 286 
 HIS   0.006   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10352)
  covalent geometry    : angle       0.56816 (14050)
  SS BOND              : bond        0.00106 (    6)
  SS BOND              : angle       0.80803 (   12)
  hydrogen bonds       : bond        0.16704 (  590)
  hydrogen bonds       : angle       6.95290 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 THR cc_start: 0.7450 (m) cc_final: 0.7236 (m)
REVERT: A  449 MET cc_start: 0.1924 (tpp) cc_final: 0.1654 (tpp)
REVERT: A  462 LEU cc_start: 0.7315 (tp) cc_final: 0.7066 (tp)
REVERT: B   69 THR cc_start: 0.7698 (m) cc_final: 0.7428 (m)
REVERT: B  457 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7230 (tttt)
REVERT: B  693 MET cc_start: 0.6619 (mmm) cc_final: 0.6103 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2637
  time to fit residues: 55.2061
Evaluate side-chains
  123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.1764

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

Flipped N/Q/H residues before XYZ refinement:
B 569 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5143 r_free = 0.5143 target = 0.308302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.282527 restraints weight = 44427.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4977 r_free = 0.4977 target = 0.289956 restraints weight = 24561.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.5022 r_free = 0.5022 target = 0.294892 restraints weight = 15526.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.5049 r_free = 0.5049 target = 0.298011 restraints weight = 10783.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.5067 r_free = 0.5067 target = 0.300086 restraints weight = 8058.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.5067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4461
moved from start:          0.1163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10358  Z= 0.158
  Angle     :  0.581   5.987  14062  Z= 0.327
  Chirality :  0.038   0.150   1586
  Planarity :  0.005   0.049   1718
  Dihedral  :  4.694  24.717   1376
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  6.48 %
    Favored  : 92.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.24), residues: 1250
  helix:  0.51 (0.18), residues: 782
  sheet:  0.74 (1.10), residues: 20
  loop : -1.06 (0.32), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 475 
 TYR   0.013   0.001   TYR B 278 
 PHE   0.030   0.002   PHE A 711 
 TRP   0.027   0.001   TRP B 286 
 HIS   0.008   0.001   HIS A 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (10352)
  covalent geometry    : angle       0.58048 (14050)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       0.69470 (   12)
  hydrogen bonds       : bond        0.05456 (  590)
  hydrogen bonds       : angle       5.27985 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  247 ARG cc_start: 0.6958 (mmt-90) cc_final: 0.6723 (mmt-90)
REVERT: B  457 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7292 (tttt)
REVERT: B  693 MET cc_start: 0.6689 (mmm) cc_final: 0.6052 (mtp)
  outliers start: 10
  outliers final: 7
  residues processed: 148
  average time/residue: 0.2412
  time to fit residues: 50.3177
Evaluate side-chains
  136 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  713 LYS
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  569 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 104 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 109 optimal weight:    0.5980
   chunk 112 optimal weight:    1.9990
   chunk 120 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5130 r_free = 0.5130 target = 0.306782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4898 r_free = 0.4898 target = 0.281349 restraints weight = 43762.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.288537 restraints weight = 24401.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.5008 r_free = 0.5008 target = 0.293260 restraints weight = 15448.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.5031 r_free = 0.5031 target = 0.295946 restraints weight = 10783.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.5053 r_free = 0.5053 target = 0.298422 restraints weight = 8240.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.5056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4507
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.122  10358  Z= 0.163
  Angle     :  0.558   6.418  14062  Z= 0.313
  Chirality :  0.038   0.148   1586
  Planarity :  0.005   0.047   1718
  Dihedral  :  4.602  24.034   1376
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  8.83 %
    Favored  : 90.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.24), residues: 1250
  helix:  0.68 (0.18), residues: 788
  sheet:  0.37 (1.05), residues: 20
  loop : -1.11 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 247 
 TYR   0.014   0.001   TYR B 278 
 PHE   0.032   0.002   PHE A 711 
 TRP   0.018   0.001   TRP B 286 
 HIS   0.021   0.002   HIS B 569 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10352)
  covalent geometry    : angle       0.55804 (14050)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       0.45017 (   12)
  hydrogen bonds       : bond        0.04915 (  590)
  hydrogen bonds       : angle       5.14415 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6672 (tp)
REVERT: B  457 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7356 (tttt)
REVERT: B  693 MET cc_start: 0.5945 (mmm) cc_final: 0.5295 (mtp)
  outliers start: 11
  outliers final: 10
  residues processed: 148
  average time/residue: 0.2585
  time to fit residues: 54.1195
Evaluate side-chains
  138 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  713 LYS
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 7 optimal weight:    0.0170
   chunk 86 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 125 optimal weight:    8.9990
   overall best weight:    2.0026

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5105 r_free = 0.5105 target = 0.303167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4858 r_free = 0.4858 target = 0.276412 restraints weight = 43714.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4924 r_free = 0.4924 target = 0.283530 restraints weight = 24095.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4970 r_free = 0.4970 target = 0.288457 restraints weight = 15344.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.291436 restraints weight = 10725.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.5012 r_free = 0.5012 target = 0.293289 restraints weight = 8160.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.5015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4645
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10358  Z= 0.193
  Angle     :  0.598   7.514  14062  Z= 0.336
  Chirality :  0.039   0.154   1586
  Planarity :  0.005   0.046   1718
  Dihedral  :  4.758  22.883   1376
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.81 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.24), residues: 1250
  helix:  0.51 (0.18), residues: 776
  sheet:  0.32 (1.09), residues: 20
  loop : -1.15 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 247 
 TYR   0.020   0.002   TYR B 278 
 PHE   0.033   0.002   PHE A 534 
 TRP   0.019   0.001   TRP B 286 
 HIS   0.018   0.002   HIS B 569 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10352)
  covalent geometry    : angle       0.59793 (14050)
  SS BOND              : bond        0.00357 (    6)
  SS BOND              : angle       0.55294 (   12)
  hydrogen bonds       : bond        0.04818 (  590)
  hydrogen bonds       : angle       5.23391 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  157 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 TYR cc_start: 0.3847 (m-80) cc_final: 0.3063 (m-10)
REVERT: B  693 MET cc_start: 0.6038 (mmm) cc_final: 0.5660 (mtp)
  outliers start: 16
  outliers final: 16
  residues processed: 150
  average time/residue: 0.2444
  time to fit residues: 51.8535
Evaluate side-chains
  145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  713 LYS
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 102 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 107 optimal weight:    0.0670
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   chunk 92 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.6126

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

Flipped N/Q/H residues before XYZ refinement:
A 223 HIS
B 223 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5110 r_free = 0.5110 target = 0.302749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4858 r_free = 0.4858 target = 0.275280 restraints weight = 44503.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4920 r_free = 0.4920 target = 0.281858 restraints weight = 25207.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.286685 restraints weight = 16692.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4988 r_free = 0.4988 target = 0.289438 restraints weight = 12137.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.5015 r_free = 0.5015 target = 0.292086 restraints weight = 9608.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.5020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4830
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  10358  Z= 0.237
  Angle     :  0.656   6.452  14062  Z= 0.372
  Chirality :  0.041   0.165   1586
  Planarity :  0.005   0.047   1718
  Dihedral  :  5.178  24.270   1376
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.44 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.24), residues: 1250
  helix:  0.13 (0.18), residues: 778
  sheet:  None (None), residues: 0
  loop : -1.29 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 475 
 TYR   0.019   0.002   TYR B 278 
 PHE   0.041   0.003   PHE A 534 
 TRP   0.021   0.002   TRP B 286 
 HIS   0.007   0.002   HIS A 723 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (10352)
  covalent geometry    : angle       0.65639 (14050)
  SS BOND              : bond        0.00368 (    6)
  SS BOND              : angle       0.70386 (   12)
  hydrogen bonds       : bond        0.05221 (  590)
  hydrogen bonds       : angle       5.59468 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  164 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 GLU cc_start: 0.6694 (mm-30) cc_final: 0.5849 (mm-30)
REVERT: B  300 ARG cc_start: 0.5570 (ttt180) cc_final: 0.5129 (ttp-170)
REVERT: B  383 TYR cc_start: 0.3953 (m-80) cc_final: 0.3043 (m-10)
REVERT: B  693 MET cc_start: 0.5937 (mmm) cc_final: 0.5511 (mtp)
  outliers start: 24
  outliers final: 21
  residues processed: 154
  average time/residue: 0.2470
  time to fit residues: 53.3562
Evaluate side-chains
  158 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  146 ASN
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  563 GLU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  713 LYS
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  563 GLU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0670
   chunk 39 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 119 optimal weight:    1.9990
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
A 569 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5128 r_free = 0.5128 target = 0.305065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4874 r_free = 0.4874 target = 0.277605 restraints weight = 44514.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4942 r_free = 0.4942 target = 0.284730 restraints weight = 24502.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4991 r_free = 0.4991 target = 0.289846 restraints weight = 15765.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.5020 r_free = 0.5020 target = 0.293164 restraints weight = 11151.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.5036 r_free = 0.5036 target = 0.295047 restraints weight = 8450.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.5038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4752
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10358  Z= 0.168
  Angle     :  0.580   6.926  14062  Z= 0.325
  Chirality :  0.038   0.151   1586
  Planarity :  0.005   0.051   1718
  Dihedral  :  4.909  23.089   1376
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 15.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.85 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.24), residues: 1250
  helix:  0.27 (0.18), residues: 792
  sheet:  None (None), residues: 0
  loop : -1.35 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 475 
 TYR   0.020   0.001   TYR B 278 
 PHE   0.033   0.002   PHE A 534 
 TRP   0.018   0.001   TRP B 286 
 HIS   0.006   0.001   HIS A 569 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (10352)
  covalent geometry    : angle       0.58026 (14050)
  SS BOND              : bond        0.00286 (    6)
  SS BOND              : angle       0.55054 (   12)
  hydrogen bonds       : bond        0.04621 (  590)
  hydrogen bonds       : angle       5.30003 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  159 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 GLU cc_start: 0.6458 (mm-30) cc_final: 0.5667 (mm-30)
REVERT: B  383 TYR cc_start: 0.3957 (m-80) cc_final: 0.3068 (m-10)
REVERT: B  693 MET cc_start: 0.6061 (mmm) cc_final: 0.5856 (mtp)
  outliers start: 17
  outliers final: 15
  residues processed: 155
  average time/residue: 0.2517
  time to fit residues: 54.6970
Evaluate side-chains
  149 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  713 LYS
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 121 optimal weight:   10.0000
   chunk 118 optimal weight:    0.0370
   chunk 10 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 24 optimal weight:    0.1980
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.9660

-------------------------------------------------------------------------------
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 = 0.5140 r_free = 0.5140 target = 0.306227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4892 r_free = 0.4892 target = 0.279514 restraints weight = 44401.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4961 r_free = 0.4961 target = 0.286615 restraints weight = 24594.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.5008 r_free = 0.5008 target = 0.291649 restraints weight = 15720.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.5036 r_free = 0.5036 target = 0.294796 restraints weight = 11063.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.5051 r_free = 0.5051 target = 0.296695 restraints weight = 8386.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.5057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4686
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      :  0.003   0.031  10358  Z= 0.139
  Angle     :  0.547   6.781  14062  Z= 0.303
  Chirality :  0.037   0.146   1586
  Planarity :  0.005   0.048   1718
  Dihedral  :  4.685  22.250   1376
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.04 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.24), residues: 1250
  helix:  0.53 (0.18), residues: 792
  sheet:  0.39 (1.19), residues: 20
  loop : -1.38 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 475 
 TYR   0.016   0.001   TYR B 278 
 PHE   0.038   0.002   PHE A 157 
 TRP   0.015   0.001   TRP B 286 
 HIS   0.003   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10352)
  covalent geometry    : angle       0.54745 (14050)
  SS BOND              : bond        0.00224 (    6)
  SS BOND              : angle       0.49196 (   12)
  hydrogen bonds       : bond        0.04253 (  590)
  hydrogen bonds       : angle       5.05026 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  161 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 GLU cc_start: 0.6372 (mm-30) cc_final: 0.5618 (mm-30)
REVERT: B  383 TYR cc_start: 0.3928 (m-80) cc_final: 0.3056 (m-10)
REVERT: B  693 MET cc_start: 0.6129 (mmm) cc_final: 0.5926 (mtp)
REVERT: B  740 MET cc_start: 0.6327 (ptp) cc_final: 0.6059 (ptp)
  outliers start: 16
  outliers final: 13
  residues processed: 155
  average time/residue: 0.2633
  time to fit residues: 57.1686
Evaluate side-chains
  147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 CYS
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 107 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 47 optimal weight:    0.3980
   chunk 119 optimal weight:    9.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B 569 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5131 r_free = 0.5131 target = 0.305357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4884 r_free = 0.4884 target = 0.278544 restraints weight = 44462.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4953 r_free = 0.4953 target = 0.285727 restraints weight = 24576.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4997 r_free = 0.4997 target = 0.290568 restraints weight = 15706.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.5027 r_free = 0.5027 target = 0.293894 restraints weight = 11117.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.5042 r_free = 0.5042 target = 0.295788 restraints weight = 8359.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.5049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4701
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10358  Z= 0.147
  Angle     :  0.554   6.469  14062  Z= 0.308
  Chirality :  0.037   0.146   1586
  Planarity :  0.005   0.050   1718
  Dihedral  :  4.617  22.332   1376
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.51 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.24), residues: 1250
  helix:  0.61 (0.18), residues: 792
  sheet:  0.31 (1.19), residues: 20
  loop : -1.36 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 247 
 TYR   0.016   0.001   TYR B 278 
 PHE   0.040   0.002   PHE A 157 
 TRP   0.016   0.001   TRP A 286 
 HIS   0.014   0.001   HIS B 569 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10352)
  covalent geometry    : angle       0.55370 (14050)
  SS BOND              : bond        0.00262 (    6)
  SS BOND              : angle       0.48866 (   12)
  hydrogen bonds       : bond        0.04191 (  590)
  hydrogen bonds       : angle       5.01576 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  156 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 GLU cc_start: 0.6458 (mm-30) cc_final: 0.5712 (mm-30)
REVERT: B  383 TYR cc_start: 0.3976 (m-80) cc_final: 0.3065 (m-10)
REVERT: B  693 MET cc_start: 0.6128 (mmm) cc_final: 0.5708 (mtp)
  outliers start: 18
  outliers final: 15
  residues processed: 151
  average time/residue: 0.2336
  time to fit residues: 49.3465
Evaluate side-chains
  146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  108 CYS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  569 HIS
Chi-restraints excluded: chain B residue  716 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   chunk 67 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 57 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 569 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5143 r_free = 0.5143 target = 0.307030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.280800 restraints weight = 44435.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4971 r_free = 0.4971 target = 0.287928 restraints weight = 24446.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.5015 r_free = 0.5015 target = 0.292740 restraints weight = 15543.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.5043 r_free = 0.5043 target = 0.295972 restraints weight = 10959.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.5057 r_free = 0.5057 target = 0.297695 restraints weight = 8244.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.5062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4654
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10358  Z= 0.127
  Angle     :  0.541   8.833  14062  Z= 0.298
  Chirality :  0.037   0.143   1586
  Planarity :  0.004   0.049   1718
  Dihedral  :  4.530  21.480   1376
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.41 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.24), residues: 1250
  helix:  0.74 (0.18), residues: 792
  sheet:  0.13 (1.15), residues: 20
  loop : -1.29 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 247 
 TYR   0.015   0.001   TYR B 278 
 PHE   0.038   0.002   PHE A 157 
 TRP   0.015   0.001   TRP A 286 
 HIS   0.023   0.001   HIS B 569 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10352)
  covalent geometry    : angle       0.54095 (14050)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       0.43216 (   12)
  hydrogen bonds       : bond        0.04014 (  590)
  hydrogen bonds       : angle       4.90701 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  158 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6810 (tp)
REVERT: A  535 GLU cc_start: 0.6387 (mm-30) cc_final: 0.5639 (mm-30)
REVERT: B  383 TYR cc_start: 0.3940 (m-80) cc_final: 0.3057 (m-10)
REVERT: B  588 THR cc_start: 0.3380 (m) cc_final: 0.3128 (m)
REVERT: B  693 MET cc_start: 0.6128 (mmm) cc_final: 0.5652 (mtp)
  outliers start: 19
  outliers final: 16
  residues processed: 152
  average time/residue: 0.2335
  time to fit residues: 49.8659
Evaluate side-chains
  153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  108 CYS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  716 LEU
Chi-restraints excluded: chain B residue  739 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 119 optimal weight:    0.2980
   chunk 37 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5129 r_free = 0.5129 target = 0.305189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.278269 restraints weight = 44347.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4951 r_free = 0.4951 target = 0.285507 restraints weight = 24425.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4997 r_free = 0.4997 target = 0.290413 restraints weight = 15532.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5018 r_free = 0.5018 target = 0.293065 restraints weight = 10969.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.5042 r_free = 0.5042 target = 0.295708 restraints weight = 8563.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.5049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4689
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10358  Z= 0.143
  Angle     :  0.539   5.757  14062  Z= 0.298
  Chirality :  0.037   0.144   1586
  Planarity :  0.004   0.050   1718
  Dihedral  :  4.534  22.419   1376
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.60 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.24), residues: 1250
  helix:  0.76 (0.18), residues: 792
  sheet:  0.14 (1.16), residues: 20
  loop : -1.33 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 247 
 TYR   0.015   0.001   TYR B 278 
 PHE   0.036   0.002   PHE A 157 
 TRP   0.017   0.001   TRP A 286 
 HIS   0.006   0.001   HIS B 569 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10352)
  covalent geometry    : angle       0.53862 (14050)
  SS BOND              : bond        0.00290 (    6)
  SS BOND              : angle       0.48029 (   12)
  hydrogen bonds       : bond        0.04005 (  590)
  hydrogen bonds       : angle       4.94928 ( 1746)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  543 is missing expected H atoms. Skipping.
Residue THR  543 is missing expected H atoms. Skipping.
Evaluate side-chains
  159 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  535 GLU cc_start: 0.6411 (mm-30) cc_final: 0.5660 (mm-30)
REVERT: B  693 MET cc_start: 0.6039 (mmm) cc_final: 0.5545 (mtp)
  outliers start: 18
  outliers final: 16
  residues processed: 152
  average time/residue: 0.2532
  time to fit residues: 54.2125
Evaluate side-chains
  153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 HIS
Chi-restraints excluded: chain A residue  108 CYS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  274 GLU
Chi-restraints excluded: chain B residue  716 LEU
Chi-restraints excluded: chain B residue  739 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 123 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 117 optimal weight:    0.9990
   chunk 112 optimal weight:    0.0980
   chunk 87 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.5134 r_free = 0.5134 target = 0.306100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4894 r_free = 0.4894 target = 0.279878 restraints weight = 44508.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.286903 restraints weight = 24333.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5007 r_free = 0.5007 target = 0.291798 restraints weight = 15542.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.5036 r_free = 0.5036 target = 0.295040 restraints weight = 10929.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.5052 r_free = 0.5052 target = 0.297069 restraints weight = 8204.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.5057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4668
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10358  Z= 0.132
  Angle     :  0.532   7.113  14062  Z= 0.295
  Chirality :  0.037   0.148   1586
  Planarity :  0.004   0.048   1718
  Dihedral  :  4.465  22.020   1376
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.70 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.24), residues: 1250
  helix:  0.80 (0.18), residues: 792
  sheet:  0.22 (1.18), residues: 20
  loop : -1.32 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 247 
 TYR   0.015   0.001   TYR B 278 
 PHE   0.035   0.002   PHE A 157 
 TRP   0.016   0.001   TRP A 286 
 HIS   0.004   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10352)
  covalent geometry    : angle       0.53187 (14050)
  SS BOND              : bond        0.00207 (    6)
  SS BOND              : angle       0.45678 (   12)
  hydrogen bonds       : bond        0.03934 (  590)
  hydrogen bonds       : angle       4.89416 ( 1746)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3336.53 seconds
wall clock time: 57 minutes 55.95 seconds (3475.95 seconds total)