Starting phenix.real_space_refine
on Tue Mar  3 15:22:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n8p_24241/03_2026/7n8p_24241.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n8p_24241/03_2026/7n8p_24241.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n8p_24241/03_2026/7n8p_24241.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n8p_24241/03_2026/7n8p_24241.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n8p_24241/03_2026/7n8p_24241.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n8p_24241/03_2026/7n8p_24241.cif"
  }
  resolution = 3.42
  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=   0.006 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4438      2.51       5
     N    1140      2.21       5
     O    1140      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6758
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3379
          Classifications: {'peptide': 450}
          Link IDs: {'PTRANS': 19, 'TRANS': 430}
    Chain: "B"
      Number of atoms: 3379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3379
          Classifications: {'peptide': 450}
          Link IDs: {'PTRANS': 19, 'TRANS': 430}
  Time building chain proxies: 1.43, per 1000 atoms: 0.21
  Number of scatterers: 6758
  At special positions: 0
  Unit cell: (76.504, 76.504, 114.232, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1140      8.00
     N    1140      7.00
     C    4438      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 260.4 milliseconds
  

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      74.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 27
      removed outlier: 3.996A  pdb=" N   GLN A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ARG A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 69
      removed outlier: 3.530A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   THR A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN A  62 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ALA A  67 " --> pdb=" O   GLN A  63 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   VAL A  69 " --> pdb=" O   MET A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 100
      removed outlier: 3.717A  pdb=" N   LEU A  79 " --> pdb=" O   TYR A  75 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG A  98 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR A 100 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 3.760A  pdb=" N   GLY A 105 " --> pdb=" O   PRO A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 116
      removed outlier: 4.172A  pdb=" N   GLY A 114 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 132
      removed outlier: 3.651A  pdb=" N   LEU A 128 " --> pdb=" O   TRP A 124 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
      removed outlier: 3.528A  pdb=" N   PHE A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 141
    Processing helix  chain 'A' and resid 148 through 165
      removed outlier: 4.047A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASP A 164 " --> pdb=" O   ARG A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 190
      removed outlier: 3.678A  pdb=" N   ARG A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   HIS A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLY A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ALA A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA A 187 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 201
      removed outlier: 3.645A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 224
      removed outlier: 3.728A  pdb=" N   ILE A 220 " --> pdb=" O   LYS A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 233
      removed outlier: 4.153A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 3.526A  pdb=" N   LEU A 252 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 281
      removed outlier: 3.531A  pdb=" N   ILE A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLY A 259 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.978A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 304
      removed outlier: 4.051A  pdb=" N   LEU A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ALA A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   CYS A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 349
      removed outlier: 3.719A  pdb=" N   PHE A 335 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   THR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 379
      removed outlier: 3.778A  pdb=" N   VAL A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 395
      removed outlier: 4.056A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 401
    Processing helix  chain 'A' and resid 404 through 417
      removed outlier: 3.627A  pdb=" N   GLY A 408 " --> pdb=" O   ALA A 404 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASP A 417 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 440
      removed outlier: 3.535A  pdb=" N   THR A 428 " --> pdb=" O   PRO A 424 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLY A 440 " --> pdb=" O   ALA A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 447
    Processing helix  chain 'A' and resid 448 through 460
      removed outlier: 4.028A  pdb=" N   ALA A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 26
      removed outlier: 4.035A  pdb=" N   ARG B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU B  26 " --> pdb=" O   ILE B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 69
      removed outlier: 3.947A  pdb=" N   MET B  38 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   TRP B  59 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   VAL B  69 " --> pdb=" O   MET B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 4.032A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LEU B  89 " --> pdb=" O   CYS B  85 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   LEU B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 116
      removed outlier: 3.629A  pdb=" N   GLY B 114 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 132
      Proline residue:  B 129  - end of helix
    Processing helix  chain 'B' and resid 134 through 141
      removed outlier: 3.653A  pdb=" N   GLY B 141 " --> pdb=" O   GLY B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 165
      removed outlier: 4.166A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.920A  pdb=" N   HIS B 175 " --> pdb=" O   ASP B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 184
    Processing helix  chain 'B' and resid 185 through 190
      removed outlier: 3.668A  pdb=" N   PHE B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 201
      removed outlier: 3.603A  pdb=" N   GLY B 196 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE B 197 " --> pdb=" O   PRO B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 233
      removed outlier: 3.752A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 252
      removed outlier: 3.748A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 281
      removed outlier: 3.601A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 4.137A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 308
      removed outlier: 3.943A  pdb=" N   LEU B 293 " --> pdb=" O   THR B 289 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLY B 306 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 348
      removed outlier: 4.099A  pdb=" N   PHE B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   THR B 343 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   LEU B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   LEU B 346 " --> pdb=" O   ILE B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 379
      removed outlier: 3.885A  pdb=" N   LEU B 363 " --> pdb=" O   PRO B 359 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL B 366 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 395
      removed outlier: 4.543A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 417
      removed outlier: 3.554A  pdb=" N   ILE B 410 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 438
      removed outlier: 3.675A  pdb=" N   THR B 433 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LEU B 434 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 448
    Processing helix  chain 'B' and resid 448 through 460
      removed outlier: 3.599A  pdb=" N   GLN B 456 " --> pdb=" O   THR B 452 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU B 457 " --> pdb=" O   LEU B 453 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)

    381 hydrogen bonds defined for protein.
    1128 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2133
        1.34 -     1.46: 1264
        1.46 -     1.57: 3431
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6902
  Sorted by residual:
  bond pdb=" C   ILE A 109 "
       pdb=" N   PRO A 110 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.049 8.40e-03 1.42e+04 3.34e+01
  bond pdb=" C   ALA A 358 "
       pdb=" N   PRO A 359 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 8.40e-03 1.42e+04 2.75e+01
  bond pdb=" C   LEU B 128 "
       pdb=" N   PRO B 129 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.62e+00
  bond pdb=" CA  ILE B 109 "
       pdb=" C   ILE B 109 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.015 8.80e-03 1.29e+04 2.85e+00
  bond pdb=" CG1 ILE A 197 "
       pdb=" CD1 ILE A 197 "
    ideal  model  delta    sigma   weight residual
    1.513  1.456  0.057 3.90e-02 6.57e+02 2.15e+00
  ... (remaining 6897 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 9106
        2.28 -     4.57: 217
        4.57 -     6.85: 35
        6.85 -     9.14: 5
        9.14 -    11.42: 3
  Bond angle restraints: 9366
  Sorted by residual:
  angle pdb=" N   LEU A 163 "
        pdb=" CA  LEU A 163 "
        pdb=" C   LEU A 163 "
      ideal   model   delta    sigma   weight residual
     114.75  104.28   10.47 1.26e+00 6.30e-01 6.90e+01
  angle pdb=" C   GLY B 108 "
        pdb=" N   ILE B 109 "
        pdb=" CA  ILE B 109 "
      ideal   model   delta    sigma   weight residual
     120.24  124.27   -4.03 6.30e-01 2.52e+00 4.09e+01
  angle pdb=" C   GLY A 108 "
        pdb=" N   ILE A 109 "
        pdb=" CA  ILE A 109 "
      ideal   model   delta    sigma   weight residual
     120.24  122.94   -2.70 6.30e-01 2.52e+00 1.83e+01
  angle pdb=" CA  LEU A 163 "
        pdb=" C   LEU A 163 "
        pdb=" N   ASP A 164 "
      ideal   model   delta    sigma   weight residual
     119.80  114.74    5.06 1.34e+00 5.57e-01 1.42e+01
  angle pdb=" C   ASN A 318 "
        pdb=" N   LEU A 319 "
        pdb=" CA  LEU A 319 "
      ideal   model   delta    sigma   weight residual
     121.54  127.98   -6.44 1.91e+00 2.74e-01 1.14e+01
  ... (remaining 9361 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 3525
       16.85 -    33.70: 391
       33.70 -    50.55: 85
       50.55 -    67.40: 7
       67.40 -    84.25: 4
  Dihedral angle restraints: 4012
    sinusoidal: 1524
      harmonic: 2488
  Sorted by residual:
  dihedral pdb=" CA  LEU A 301 "
           pdb=" C   LEU A 301 "
           pdb=" N   CYS A 302 "
           pdb=" CA  CYS A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.80   28.20     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  VAL B 162 "
           pdb=" C   VAL B 162 "
           pdb=" N   LEU B 163 "
           pdb=" CA  LEU B 163 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.53   27.47     0      5.00e+00 4.00e-02 3.02e+01
  dihedral pdb=" CA  PHE A 317 "
           pdb=" C   PHE A 317 "
           pdb=" N   ASN A 318 "
           pdb=" CA  ASN A 318 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.45   23.55     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 4009 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 922
       0.065 -    0.131: 162
       0.131 -    0.196: 15
       0.196 -    0.261: 1
       0.261 -    0.327: 2
  Chirality restraints: 1102
  Sorted by residual:
  chirality pdb=" CB  ILE A 356 "
            pdb=" CA  ILE A 356 "
            pdb=" CG1 ILE A 356 "
            pdb=" CG2 ILE A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CB  VAL A 162 "
            pdb=" CA  VAL A 162 "
            pdb=" CG1 VAL A 162 "
            pdb=" CG2 VAL A 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  VAL A  41 "
            pdb=" CA  VAL A  41 "
            pdb=" CG1 VAL A  41 "
            pdb=" CG2 VAL A  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.80e-01
  ... (remaining 1099 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  75 "   -0.049 5.00e-02 4.00e+02   7.33e-02 8.59e+00
        pdb=" N   PRO A  76 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A  76 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A  76 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 423 "    0.042 5.00e-02 4.00e+02   6.21e-02 6.18e+00
        pdb=" N   PRO B 424 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B 424 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 424 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 266 "   -0.038 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO B 267 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 267 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 267 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1834
        2.80 -     3.33: 6031
        3.33 -     3.85: 11095
        3.85 -     4.38: 13324
        4.38 -     4.90: 22660
  Nonbonded interactions: 54944
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 345 "
            pdb=" OG  SER B 349 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR B  94 "
            pdb=" OG  SER B 350 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG  SER A  86 "
            pdb=" O   GLY A 141 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   VAL B 412 "
            pdb=" OG1 THR B 416 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   LEU B 435 "
            pdb=" OG1 THR B 439 "
     model   vdw
     2.311 3.040
  ... (remaining 54939 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain '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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.920
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
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      :  0.005   0.071   6902  Z= 0.242
  Angle     :  0.891  11.422   9366  Z= 0.504
  Chirality :  0.051   0.327   1102
  Planarity :  0.008   0.073   1176
  Dihedral  : 14.416  84.252   2440
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  9.44 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.50 (0.20), residues: 896
  helix: -3.60 (0.13), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.91 (0.37), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  64 
 TYR   0.018   0.002   TYR B 419 
 PHE   0.025   0.002   PHE B 219 
 TRP   0.008   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 6902)
  covalent geometry    : angle       0.89101 ( 9366)
  hydrogen bonds       : bond        0.16501 (  381)
  hydrogen bonds       : angle       6.63065 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  167 ARG cc_start: 0.7064 (mtt90) cc_final: 0.6831 (mtm180)
REVERT: B   38 MET cc_start: 0.7506 (mmt) cc_final: 0.7300 (mmt)
  outliers start: 2
  outliers final: 1
  residues processed: 106
  average time/residue: 0.0736
  time to fit residues: 10.9302
Evaluate side-chains
  79 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0980
   chunk 74 optimal weight:    0.0570
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
A 460 GLN
B  61 GLN
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 HIS
B 284 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.138245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.122800 restraints weight = 9569.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.62
r_work: 0.3426 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6902  Z= 0.110
  Angle     :  0.554   8.969   9366  Z= 0.282
  Chirality :  0.040   0.139   1102
  Planarity :  0.005   0.044   1176
  Dihedral  :  5.292  34.735    962
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.01 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.35 (0.26), residues: 896
  helix: -2.09 (0.18), residues: 676
  sheet:  None (None), residues: 0
  loop : -1.91 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 147 
 TYR   0.005   0.001   TYR A 419 
 PHE   0.013   0.001   PHE B 307 
 TRP   0.007   0.001   TRP A  59 
 HIS   0.002   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6902)
  covalent geometry    : angle       0.55440 ( 9366)
  hydrogen bonds       : bond        0.03298 (  381)
  hydrogen bonds       : angle       3.99972 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  110 PRO cc_start: 0.9135 (Cg_endo) cc_final: 0.8846 (Cg_exo)
REVERT: B   38 MET cc_start: 0.8509 (mmt) cc_final: 0.8203 (mmt)
  outliers start: 9
  outliers final: 4
  residues processed: 91
  average time/residue: 0.0548
  time to fit residues: 7.5571
Evaluate side-chains
  82 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue  180 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 86 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 60 optimal weight:    0.3980
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 284 HIS
B 157 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.141825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.125086 restraints weight = 9774.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.76
r_work: 0.3412 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6902  Z= 0.114
  Angle     :  0.536   8.436   9366  Z= 0.269
  Chirality :  0.040   0.134   1102
  Planarity :  0.004   0.042   1176
  Dihedral  :  4.964  34.270    962
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.04 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.28), residues: 896
  helix: -1.38 (0.20), residues: 674
  sheet:  None (None), residues: 0
  loop : -1.68 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 147 
 TYR   0.015   0.001   TYR B 419 
 PHE   0.012   0.001   PHE B 307 
 TRP   0.005   0.001   TRP B 124 
 HIS   0.001   0.000   HIS B 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6902)
  covalent geometry    : angle       0.53616 ( 9366)
  hydrogen bonds       : bond        0.03031 (  381)
  hydrogen bonds       : angle       3.69533 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  110 PRO cc_start: 0.9124 (Cg_endo) cc_final: 0.8826 (Cg_exo)
REVERT: A  373 MET cc_start: 0.8019 (ttm) cc_final: 0.7805 (mtt)
REVERT: A  414 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8124 (mm-30)
REVERT: A  421 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8012 (pp)
REVERT: B   38 MET cc_start: 0.8607 (mmt) cc_final: 0.8245 (mmt)
REVERT: B   74 ASN cc_start: 0.8597 (t0) cc_final: 0.8350 (t0)
REVERT: B  419 TYR cc_start: 0.7971 (t80) cc_final: 0.7481 (t80)
  outliers start: 11
  outliers final: 5
  residues processed: 91
  average time/residue: 0.0559
  time to fit residues: 7.8031
Evaluate side-chains
  85 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue  180 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 57 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 24 optimal weight:    0.6980
   chunk 64 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.140517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.123484 restraints weight = 9890.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.78
r_work: 0.3388 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6902  Z= 0.130
  Angle     :  0.545   7.892   9366  Z= 0.272
  Chirality :  0.040   0.138   1102
  Planarity :  0.004   0.044   1176
  Dihedral  :  4.856  33.941    962
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 17.70 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.29), residues: 896
  helix: -1.06 (0.20), residues: 674
  sheet:  None (None), residues: 0
  loop : -1.53 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 147 
 TYR   0.009   0.001   TYR A 419 
 PHE   0.016   0.001   PHE A 379 
 TRP   0.006   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6902)
  covalent geometry    : angle       0.54451 ( 9366)
  hydrogen bonds       : bond        0.02964 (  381)
  hydrogen bonds       : angle       3.65246 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  110 PRO cc_start: 0.9101 (Cg_endo) cc_final: 0.8816 (Cg_exo)
REVERT: A  373 MET cc_start: 0.8066 (ttm) cc_final: 0.7813 (mtt)
REVERT: A  394 MET cc_start: 0.8665 (ttp) cc_final: 0.8429 (ttp)
REVERT: A  414 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8085 (mm-30)
REVERT: A  421 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8149 (pp)
REVERT: B   38 MET cc_start: 0.8649 (mmt) cc_final: 0.8304 (mmt)
REVERT: B   74 ASN cc_start: 0.8605 (t0) cc_final: 0.8314 (t0)
REVERT: B  136 LEU cc_start: 0.7938 (tp) cc_final: 0.7712 (tp)
REVERT: B  419 TYR cc_start: 0.8073 (t80) cc_final: 0.7588 (t80)
  outliers start: 9
  outliers final: 5
  residues processed: 85
  average time/residue: 0.0545
  time to fit residues: 7.1089
Evaluate side-chains
  83 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue  264 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0000
   chunk 58 optimal weight:    0.0060
   chunk 47 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.5004

-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.143252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.126396 restraints weight = 9822.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.75
r_work: 0.3429 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6902  Z= 0.097
  Angle     :  0.522   8.007   9366  Z= 0.258
  Chirality :  0.039   0.133   1102
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.656  35.145    962
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.14 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.29), residues: 896
  helix: -0.70 (0.21), residues: 674
  sheet:  None (None), residues: 0
  loop : -1.37 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 147 
 TYR   0.007   0.001   TYR B  94 
 PHE   0.013   0.001   PHE A 379 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 6902)
  covalent geometry    : angle       0.52207 ( 9366)
  hydrogen bonds       : bond        0.02705 (  381)
  hydrogen bonds       : angle       3.50896 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  110 PRO cc_start: 0.9058 (Cg_endo) cc_final: 0.8788 (Cg_exo)
REVERT: A  414 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7946 (mm-30)
REVERT: A  421 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8039 (pp)
REVERT: B   38 MET cc_start: 0.8590 (mmt) cc_final: 0.8177 (mmt)
REVERT: B   74 ASN cc_start: 0.8585 (t0) cc_final: 0.8326 (t0)
REVERT: B   78 LEU cc_start: 0.8675 (tt) cc_final: 0.8399 (tt)
REVERT: B  136 LEU cc_start: 0.7784 (tp) cc_final: 0.7575 (tp)
REVERT: B  223 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7796 (mt)
REVERT: B  419 TYR cc_start: 0.7973 (t80) cc_final: 0.7508 (t80)
  outliers start: 15
  outliers final: 7
  residues processed: 103
  average time/residue: 0.0552
  time to fit residues: 8.6174
Evaluate side-chains
  92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0470
   chunk 56 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
B 153 GLN
B 157 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.143151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.126270 restraints weight = 9855.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.76
r_work: 0.3429 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6902  Z= 0.103
  Angle     :  0.529  10.179   9366  Z= 0.261
  Chirality :  0.039   0.133   1102
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.555  34.215    962
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.29 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.30), residues: 896
  helix: -0.50 (0.21), residues: 674
  sheet:  None (None), residues: 0
  loop : -1.27 (0.46), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 147 
 TYR   0.007   0.001   TYR B 255 
 PHE   0.017   0.001   PHE B 307 
 TRP   0.006   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 6902)
  covalent geometry    : angle       0.52921 ( 9366)
  hydrogen bonds       : bond        0.02698 (  381)
  hydrogen bonds       : angle       3.48727 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  110 PRO cc_start: 0.8954 (Cg_endo) cc_final: 0.8645 (Cg_exo)
REVERT: A  414 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8156 (mm-30)
REVERT: A  421 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8086 (pp)
REVERT: A  461 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7984 (pp)
REVERT: B   38 MET cc_start: 0.8595 (mmt) cc_final: 0.8213 (mmt)
REVERT: B  223 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7790 (mt)
  outliers start: 22
  outliers final: 14
  residues processed: 100
  average time/residue: 0.0507
  time to fit residues: 7.9316
Evaluate side-chains
  95 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0270
   chunk 0 optimal weight:   10.0000
   chunk 81 optimal weight:    0.1980
   chunk 82 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.143869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.126922 restraints weight = 9675.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.78
r_work: 0.3421 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6902  Z= 0.098
  Angle     :  0.526   9.438   9366  Z= 0.259
  Chirality :  0.039   0.132   1102
  Planarity :  0.004   0.044   1176
  Dihedral  :  4.470  33.829    962
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.62 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.30), residues: 896
  helix: -0.29 (0.21), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.23 (0.45), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 147 
 TYR   0.025   0.001   TYR B 419 
 PHE   0.015   0.001   PHE B 307 
 TRP   0.004   0.000   TRP B 253 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6902)
  covalent geometry    : angle       0.52561 ( 9366)
  hydrogen bonds       : bond        0.02625 (  381)
  hydrogen bonds       : angle       3.43083 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  414 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7914 (mm-30)
REVERT: A  421 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8091 (pp)
REVERT: A  461 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7953 (pp)
REVERT: B   38 MET cc_start: 0.8601 (mmt) cc_final: 0.8161 (mmt)
  outliers start: 17
  outliers final: 12
  residues processed: 99
  average time/residue: 0.0540
  time to fit residues: 8.2033
Evaluate side-chains
  93 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.139144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.122172 restraints weight = 9952.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.76
r_work: 0.3372 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6902  Z= 0.164
  Angle     :  0.580   9.781   9366  Z= 0.285
  Chirality :  0.042   0.140   1102
  Planarity :  0.004   0.047   1176
  Dihedral  :  4.654  31.407    962
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.17 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.29), residues: 896
  helix: -0.45 (0.21), residues: 674
  sheet:  None (None), residues: 0
  loop : -1.26 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 147 
 TYR   0.027   0.001   TYR B 419 
 PHE   0.015   0.001   PHE B 307 
 TRP   0.007   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 6902)
  covalent geometry    : angle       0.57967 ( 9366)
  hydrogen bonds       : bond        0.02993 (  381)
  hydrogen bonds       : angle       3.62469 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  414 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7950 (mm-30)
REVERT: A  461 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7905 (pp)
REVERT: B   38 MET cc_start: 0.8670 (mmt) cc_final: 0.8235 (mmt)
REVERT: B  419 TYR cc_start: 0.7965 (t80) cc_final: 0.7725 (t80)
  outliers start: 19
  outliers final: 11
  residues processed: 92
  average time/residue: 0.0494
  time to fit residues: 7.0531
Evaluate side-chains
  87 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.141639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.124634 restraints weight = 9857.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.77
r_work: 0.3406 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6902  Z= 0.113
  Angle     :  0.548   9.419   9366  Z= 0.270
  Chirality :  0.040   0.135   1102
  Planarity :  0.004   0.045   1176
  Dihedral  :  4.416  33.186    960
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.21 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.30), residues: 896
  helix: -0.22 (0.21), residues: 672
  sheet:  None (None), residues: 0
  loop : -1.24 (0.45), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 147 
 TYR   0.021   0.001   TYR B 419 
 PHE   0.016   0.001   PHE B 307 
 TRP   0.005   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6902)
  covalent geometry    : angle       0.54766 ( 9366)
  hydrogen bonds       : bond        0.02765 (  381)
  hydrogen bonds       : angle       3.52654 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  461 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7851 (pp)
REVERT: B   38 MET cc_start: 0.8625 (mmt) cc_final: 0.8194 (mmt)
  outliers start: 16
  outliers final: 11
  residues processed: 93
  average time/residue: 0.0463
  time to fit residues: 6.7288
Evaluate side-chains
  88 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 MET
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 78 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 75 optimal weight:    0.0370
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.143031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.126115 restraints weight = 9820.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.76
r_work: 0.3425 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6902  Z= 0.107
  Angle     :  0.555  10.392   9366  Z= 0.273
  Chirality :  0.040   0.133   1102
  Planarity :  0.004   0.046   1176
  Dihedral  :  4.317  33.295    960
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.50 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.30), residues: 896
  helix: -0.02 (0.21), residues: 670
  sheet:  None (None), residues: 0
  loop : -1.16 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 147 
 TYR   0.011   0.001   TYR B 419 
 PHE   0.016   0.001   PHE B 307 
 TRP   0.005   0.000   TRP B 253 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6902)
  covalent geometry    : angle       0.55519 ( 9366)
  hydrogen bonds       : bond        0.02687 (  381)
  hydrogen bonds       : angle       3.48016 ( 1128)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  414 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7877 (mm-30)
REVERT: A  461 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7854 (pp)
REVERT: B   38 MET cc_start: 0.8604 (mmt) cc_final: 0.8158 (mmt)
REVERT: B  419 TYR cc_start: 0.7577 (t80) cc_final: 0.7087 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 89
  average time/residue: 0.0519
  time to fit residues: 7.1839
Evaluate side-chains
  89 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 64 optimal weight:    7.9990
   chunk 79 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.143218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.126272 restraints weight = 9758.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.76
r_work: 0.3426 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6902  Z= 0.107
  Angle     :  0.553  11.001   9366  Z= 0.270
  Chirality :  0.040   0.134   1102
  Planarity :  0.004   0.046   1176
  Dihedral  :  4.285  32.998    960
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.35 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.30), residues: 896
  helix:  0.10 (0.22), residues: 670
  sheet:  None (None), residues: 0
  loop : -1.15 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 147 
 TYR   0.009   0.001   TYR B 419 
 PHE   0.014   0.001   PHE B 307 
 TRP   0.005   0.001   TRP B 253 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6902)
  covalent geometry    : angle       0.55262 ( 9366)
  hydrogen bonds       : bond        0.02674 (  381)
  hydrogen bonds       : angle       3.46731 ( 1128)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1384.56 seconds
wall clock time: 24 minutes 26.18 seconds (1466.18 seconds total)