Starting phenix.real_space_refine
on Fri Aug 22 17:31:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ga3_29885/08_2025/8ga3_29885.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ga3_29885/08_2025/8ga3_29885.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ga3_29885/08_2025/8ga3_29885.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ga3_29885/08_2025/8ga3_29885.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ga3_29885/08_2025/8ga3_29885.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ga3_29885/08_2025/8ga3_29885.cif"
  }
  resolution = 3.1
  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=   0.005 sd=   0.090
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      42      5.16       5
     Cl      4      4.86       5
     C    4336      2.51       5
     N    1085      2.21       5
     O    1123      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 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: 6590
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3295
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 3291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3291
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.29, per 1000 atoms: 0.20
  Number of scatterers: 6590
  At special positions: 0
  Unit cell: (73.425, 89.925, 110.55, 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)
     Cl      4     17.00
     S      42     16.00
     O    1123      8.00
     N    1085      7.00
     C    4336      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 230 " - pdb=" SG  CYS B 249 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 249 " - pdb=" SG  CYS B 230 " 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: 0.33
  Conformation dependent library (CDL) restraints added in 443.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 0 sheets defined
      72.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 28
      removed outlier: 3.655A  pdb=" N   ARG A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLN A  24 " --> pdb=" O   GLN A  20 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LEU A  26 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLU A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   ARG A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 49
      removed outlier: 3.814A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLY A  47 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 58
    Processing helix  chain 'A' and resid 60 through 64
      removed outlier: 3.733A  pdb=" N   ARG A  64 " --> pdb=" O   GLN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 4.019A  pdb=" N   THR A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 102 through 105
      removed outlier: 3.615A  pdb=" N   GLY A 105 " --> pdb=" O   PRO A 102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 102 through 105'
    Processing helix  chain 'A' and resid 109 through 114
    Processing helix  chain 'A' and resid 123 through 139
      removed outlier: 3.596A  pdb=" N   LEU A 128 " --> pdb=" O   TRP A 124 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
      removed outlier: 3.564A  pdb=" N   PHE A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 166
      removed outlier: 3.888A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 190
      removed outlier: 3.677A  pdb=" N   ALA A 179 " --> pdb=" O   HIS A 175 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 202
      removed outlier: 3.899A  pdb=" N   ILE A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 231
      removed outlier: 3.570A  pdb=" N   SER A 225 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   MET A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TYR A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 280
      Proline residue:  A 267  - end of helix
    Processing helix  chain 'A' and resid 280 through 285
      removed outlier: 4.065A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.752A  pdb=" N   VAL A 292 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 309
      removed outlier: 3.654A  pdb=" N   LEU A 304 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 326
      removed outlier: 3.532A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 348
      removed outlier: 4.708A  pdb=" N   ARG A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 351
      No H-bonds generated for 'chain 'A' and resid 349 through 351'
    Processing helix  chain 'A' and resid 358 through 363
    Processing helix  chain 'A' and resid 363 through 379
      removed outlier: 3.647A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 401
      removed outlier: 3.590A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA A 396 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LEU A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   LEU A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA A 399 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 417
    Processing helix  chain 'A' and resid 422 through 439
      removed outlier: 3.516A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 457
      removed outlier: 3.706A  pdb=" N   LEU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 67
      removed outlier: 3.559A  pdb=" N   PHE B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TRP B  59 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   MET B  65 " --> pdb=" O   GLN B  61 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA B  67 " --> pdb=" O   GLN B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 99
      removed outlier: 4.236A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU B  89 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 117
      removed outlier: 4.223A  pdb=" N   ALA B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLU B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 132
      Proline residue:  B 129  - end of helix
      removed outlier: 3.667A  pdb=" N   PHE B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 139
    Processing helix  chain 'B' and resid 140 through 142
      No H-bonds generated for 'chain 'B' and resid 140 through 142'
    Processing helix  chain 'B' and resid 148 through 166
      removed outlier: 3.591A  pdb=" N   VAL B 152 " --> pdb=" O   GLU B 148 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG B 160 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 188
      removed outlier: 3.629A  pdb=" N   LEU B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA B 179 " --> pdb=" O   HIS B 175 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA B 182 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 3.775A  pdb=" N   ILE B 197 " --> pdb=" O   PRO B 193 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 231
      removed outlier: 3.575A  pdb=" N   PHE B 219 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ILE B 231 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 280
      Proline residue:  B 267  - end of helix
      removed outlier: 3.866A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 309
      removed outlier: 3.873A  pdb=" N   GLY B 306 " --> pdb=" O   CYS B 302 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   PHE B 307 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL B 308 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 324
      removed outlier: 3.587A  pdb=" N   THR B 324 " --> pdb=" O   ILE B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 346
      removed outlier: 3.516A  pdb=" N   PHE B 335 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   THR B 343 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 351
      removed outlier: 3.528A  pdb=" N   SER B 350 " --> pdb=" O   CYS B 347 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY B 351 " --> pdb=" O   PHE B 348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 347 through 351'
    Processing helix  chain 'B' and resid 357 through 362
    Processing helix  chain 'B' and resid 363 through 373
      removed outlier: 3.661A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 383
      removed outlier: 3.707A  pdb=" N   TYR B 382 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   HIS B 383 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 379 through 383'
    Processing helix  chain 'B' and resid 387 through 395
      removed outlier: 4.002A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 401
    Processing helix  chain 'B' and resid 411 through 417
    Processing helix  chain 'B' and resid 418 through 422
    Processing helix  chain 'B' and resid 423 through 440
      removed outlier: 3.679A  pdb=" N   ALA B 432 " --> pdb=" O   THR B 428 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B 433 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 461
      removed outlier: 3.776A  pdb=" N   LEU B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA B 454 " --> pdb=" O   ALA B 450 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU B 461 " --> pdb=" O   GLU B 457 " (cutoff:3.500A)

    336 hydrogen bonds defined for protein.
    999 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: 0.96

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2062
        1.34 -     1.46: 1227
        1.46 -     1.57: 3365
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 6730
  Sorted by residual:
  bond pdb=" C   THR B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.336  1.385 -0.049 1.23e-02 6.61e+03 1.59e+01
  bond pdb=" CA  ILE B 109 "
       pdb=" C   ILE B 109 "
    ideal  model  delta    sigma   weight residual
    1.520  1.533 -0.013 8.80e-03 1.29e+04 2.26e+00
  bond pdb=" C   ILE A 109 "
       pdb=" N   PRO A 110 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.018 1.25e-02 6.40e+03 2.01e+00
  bond pdb=" C   LEU B 423 "
       pdb=" N   PRO B 424 "
    ideal  model  delta    sigma   weight residual
    1.336  1.353 -0.017 1.25e-02 6.40e+03 1.81e+00
  bond pdb=" C   ARG B 205 "
       pdb=" N   PRO B 206 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 9.40e-03 1.13e+04 1.74e+00
  ... (remaining 6725 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 8799
        2.00 -     4.00: 278
        4.00 -     6.00: 41
        6.00 -     8.00: 24
        8.00 -    10.00: 5
  Bond angle restraints: 9147
  Sorted by residual:
  angle pdb=" N   LEU B 411 "
        pdb=" CA  LEU B 411 "
        pdb=" C   LEU B 411 "
      ideal   model   delta    sigma   weight residual
     114.62  108.19    6.43 1.14e+00 7.69e-01 3.18e+01
  angle pdb=" C   LEU B 319 "
        pdb=" N   ILE B 320 "
        pdb=" CA  ILE B 320 "
      ideal   model   delta    sigma   weight residual
     120.33  123.85   -3.52 8.00e-01 1.56e+00 1.94e+01
  angle pdb=" CA  ILE B 320 "
        pdb=" C   ILE B 320 "
        pdb=" N   PRO B 321 "
      ideal   model   delta    sigma   weight residual
     120.83  123.41   -2.58 6.10e-01 2.69e+00 1.79e+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  122.73   -2.49 6.30e-01 2.52e+00 1.57e+01
  angle pdb=" C   THR B 211 "
        pdb=" N   LEU B 212 "
        pdb=" CA  LEU B 212 "
      ideal   model   delta    sigma   weight residual
     121.54  129.01   -7.47 1.91e+00 2.74e-01 1.53e+01
  ... (remaining 9142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3426
       17.85 -    35.70: 395
       35.70 -    53.55: 59
       53.55 -    71.40: 10
       71.40 -    89.24: 3
  Dihedral angle restraints: 3893
    sinusoidal: 1447
      harmonic: 2446
  Sorted by residual:
  dihedral pdb=" CB  CYS A 230 "
           pdb=" SG  CYS A 230 "
           pdb=" SG  CYS B 249 "
           pdb=" CB  CYS B 249 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.98  -60.98     1      1.00e+01 1.00e-02 4.94e+01
  dihedral pdb=" CA  CYS A 249 "
           pdb=" C   CYS A 249 "
           pdb=" N   ASN A 250 "
           pdb=" CA  ASN A 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.86   27.14     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  ASP A 118 "
           pdb=" C   ASP A 118 "
           pdb=" N   GLN A 119 "
           pdb=" CA  GLN A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.25  -26.75     0      5.00e+00 4.00e-02 2.86e+01
  ... (remaining 3890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 891
       0.063 -    0.125: 169
       0.125 -    0.188: 18
       0.188 -    0.250: 4
       0.250 -    0.313: 2
  Chirality restraints: 1084
  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    2.33    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CB  THR B  31 "
            pdb=" CA  THR B  31 "
            pdb=" OG1 THR B  31 "
            pdb=" CG2 THR B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.30    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  THR B  31 "
            pdb=" N   THR B  31 "
            pdb=" C   THR B  31 "
            pdb=" CB  THR B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1081 not shown)

  Planarity restraints: 1147
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 358 "    0.045 5.00e-02 4.00e+02   6.66e-02 7.09e+00
        pdb=" N   PRO B 359 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 359 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 359 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 266 "    0.043 5.00e-02 4.00e+02   6.56e-02 6.88e+00
        pdb=" N   PRO A 267 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 423 "   -0.043 5.00e-02 4.00e+02   6.41e-02 6.56e+00
        pdb=" N   PRO A 424 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 424 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 424 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1144 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2042
        2.81 -     3.34: 5683
        3.34 -     3.86: 11120
        3.86 -     4.38: 13691
        4.38 -     4.90: 22872
  Nonbonded interactions: 55408
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  94 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ARG A 147 "
            pdb=" OG1 THR A 151 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   LEU B 435 "
            pdb=" OG1 THR B 439 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG  SER B  86 "
            pdb=" O   GLY B 141 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   LEU A 345 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.327 3.040
  ... (remaining 55403 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 19 through 20 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 21 through 502))
  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:             1.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.320
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
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   0.052   6732  Z= 0.202
  Angle     :  0.891   9.996   9151  Z= 0.472
  Chirality :  0.051   0.313   1084
  Planarity :  0.007   0.067   1147
  Dihedral  : 14.759  89.245   2343
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  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 aren not related in a simple way.
  whole: -6.60 (0.16), residues: 882
  helix: -4.64 (0.08), residues: 604
  sheet:  None (None), residues: 0
  loop : -3.13 (0.29), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  64 
 TYR   0.019   0.002   TYR A 210 
 PHE   0.009   0.001   PHE A 219 
 TRP   0.038   0.001   TRP B 291 
 HIS   0.007   0.002   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 6730)
  covalent geometry    : angle       0.88834 ( 9147)
  SS BOND              : bond        0.00150 (    2)
  SS BOND              : angle       3.19013 (    4)
  hydrogen bonds       : bond        0.31015 (  336)
  hydrogen bonds       : angle      12.35050 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.8663 (m-30) cc_final: 0.8459 (m-30)
REVERT: A  174 ARG cc_start: 0.6750 (mtt180) cc_final: 0.6544 (mtp180)
REVERT: B  290 LYS cc_start: 0.7985 (mttp) cc_final: 0.7784 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0904
  time to fit residues: 11.4151
Evaluate side-chains
  74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
B  70 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 = 0.3856 r_free = 0.3856 target = 0.164932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.137611 restraints weight = 7376.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 1.89
r_work: 0.3482 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6732  Z= 0.132
  Angle     :  0.620   6.486   9151  Z= 0.316
  Chirality :  0.042   0.154   1084
  Planarity :  0.006   0.046   1147
  Dihedral  :  5.491  24.908    934
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.93 %
    Favored  : 87.86 %
  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 aren not related in a simple way.
  whole: -4.55 (0.22), residues: 882
  helix: -2.84 (0.16), residues: 630
  sheet:  None (None), residues: 0
  loop : -2.91 (0.32), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 167 
 TYR   0.009   0.001   TYR A 210 
 PHE   0.007   0.001   PHE A 379 
 TRP   0.018   0.001   TRP B 291 
 HIS   0.004   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6730)
  covalent geometry    : angle       0.61916 ( 9147)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       1.96349 (    4)
  hydrogen bonds       : bond        0.04320 (  336)
  hydrogen bonds       : angle       5.65135 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7789 (mtt-85) cc_final: 0.7117 (mtm-85)
REVERT: A  147 ARG cc_start: 0.7816 (ptt-90) cc_final: 0.7438 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6745 (mtt180) cc_final: 0.5909 (mtp180)
REVERT: A  186 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8248 (mp)
REVERT: A  294 MET cc_start: 0.7192 (ttp) cc_final: 0.6654 (ttt)
  outliers start: 8
  outliers final: 2
  residues processed: 77
  average time/residue: 0.0879
  time to fit residues: 9.1265
Evaluate side-chains
  71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   chunk 84 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    0.2980
   chunk 73 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.165042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.137803 restraints weight = 7288.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.87
r_work: 0.3388 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6732  Z= 0.120
  Angle     :  0.581   7.271   9151  Z= 0.289
  Chirality :  0.041   0.130   1084
  Planarity :  0.004   0.043   1147
  Dihedral  :  5.189  24.369    934
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.44 %
    Favored  : 85.89 %
  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 aren not related in a simple way.
  whole: -3.17 (0.25), residues: 882
  helix: -1.73 (0.19), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.69 (0.33), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  64 
 TYR   0.008   0.001   TYR B  94 
 PHE   0.006   0.001   PHE A 379 
 TRP   0.014   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6730)
  covalent geometry    : angle       0.57756 ( 9147)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       2.88120 (    4)
  hydrogen bonds       : bond        0.03306 (  336)
  hydrogen bonds       : angle       4.72551 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.6996 (mtt90)
REVERT: A  147 ARG cc_start: 0.7878 (ptt-90) cc_final: 0.7459 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6768 (mtt180) cc_final: 0.5989 (mtp180)
REVERT: A  294 MET cc_start: 0.7215 (ttp) cc_final: 0.6743 (ttt)
REVERT: B   91 MET cc_start: 0.7620 (mtp) cc_final: 0.7409 (mtt)
REVERT: B  198 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7428 (mp)
  outliers start: 11
  outliers final: 4
  residues processed: 77
  average time/residue: 0.0681
  time to fit residues: 7.0885
Evaluate side-chains
  71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  198 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 82 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.168864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.143502 restraints weight = 7234.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.76
r_work: 0.3391 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6732  Z= 0.138
  Angle     :  0.582   7.626   9151  Z= 0.288
  Chirality :  0.042   0.145   1084
  Planarity :  0.004   0.047   1147
  Dihedral  :  5.120  24.288    934
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.51 %
    Favored  : 84.52 %
  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 aren not related in a simple way.
  whole: -2.54 (0.27), residues: 882
  helix: -1.18 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.68 (0.33), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  64 
 TYR   0.008   0.001   TYR A 210 
 PHE   0.006   0.001   PHE B 307 
 TRP   0.012   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6730)
  covalent geometry    : angle       0.58021 ( 9147)
  SS BOND              : bond        0.00278 (    2)
  SS BOND              : angle       2.48746 (    4)
  hydrogen bonds       : bond        0.03211 (  336)
  hydrogen bonds       : angle       4.49813 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.6988 (mtt90)
REVERT: A  147 ARG cc_start: 0.7964 (ptt-90) cc_final: 0.7519 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6786 (mtt180) cc_final: 0.5936 (mtp180)
REVERT: A  294 MET cc_start: 0.7290 (ttp) cc_final: 0.6748 (ttp)
REVERT: B   65 MET cc_start: 0.7534 (mmt) cc_final: 0.7056 (mmm)
REVERT: B   91 MET cc_start: 0.7661 (mtp) cc_final: 0.7446 (mtt)
REVERT: B  198 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7435 (mp)
  outliers start: 13
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0858
  time to fit residues: 9.2960
Evaluate side-chains
  73 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  198 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0370
   chunk 18 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.8660

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.161392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.133740 restraints weight = 7417.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.90
r_work: 0.3352 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6732  Z= 0.144
  Angle     :  0.622  14.365   9151  Z= 0.306
  Chirality :  0.043   0.164   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  5.191  27.705    934
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.26 %
    Favored  : 83.76 %
  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 aren not related in a simple way.
  whole: -2.22 (0.27), residues: 882
  helix: -0.93 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.61 (0.34), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  64 
 TYR   0.011   0.001   TYR A 229 
 PHE   0.018   0.001   PHE B  95 
 TRP   0.012   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6730)
  covalent geometry    : angle       0.60830 ( 9147)
  SS BOND              : bond        0.00436 (    2)
  SS BOND              : angle       6.27069 (    4)
  hydrogen bonds       : bond        0.03222 (  336)
  hydrogen bonds       : angle       4.41889 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.7960 (ptt-90) cc_final: 0.7520 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6764 (mtt180) cc_final: 0.5880 (mtp180)
REVERT: A  294 MET cc_start: 0.7225 (ttp) cc_final: 0.6682 (ttp)
REVERT: B   65 MET cc_start: 0.7492 (mmt) cc_final: 0.7114 (mmm)
REVERT: B   91 MET cc_start: 0.7686 (mtp) cc_final: 0.7454 (mtt)
REVERT: B  198 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7414 (mp)
REVERT: B  233 ASN cc_start: 0.7902 (m110) cc_final: 0.7464 (m110)
  outliers start: 13
  outliers final: 9
  residues processed: 77
  average time/residue: 0.0953
  time to fit residues: 10.1703
Evaluate side-chains
  73 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0060
   chunk 54 optimal weight:    0.8980
   chunk 74 optimal weight:    0.4980
   chunk 64 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.164269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.136562 restraints weight = 7345.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3585 rms_B_bonded: 1.89
r_work: 0.3465 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6732  Z= 0.120
  Angle     :  0.591  12.250   9151  Z= 0.291
  Chirality :  0.042   0.149   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  5.045  25.270    934
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.72 %
    Favored  : 83.46 %
  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 aren not related in a simple way.
  whole: -1.90 (0.28), residues: 882
  helix: -0.68 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -2.54 (0.34), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 167 
 TYR   0.007   0.001   TYR A 229 
 PHE   0.020   0.001   PHE B  95 
 TRP   0.012   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6730)
  covalent geometry    : angle       0.57998 ( 9147)
  SS BOND              : bond        0.00116 (    2)
  SS BOND              : angle       5.53194 (    4)
  hydrogen bonds       : bond        0.03019 (  336)
  hydrogen bonds       : angle       4.22893 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  147 ARG cc_start: 0.7873 (ptt-90) cc_final: 0.7440 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6767 (mtt180) cc_final: 0.5868 (mtp180)
REVERT: A  294 MET cc_start: 0.7226 (ttp) cc_final: 0.6679 (ttp)
REVERT: B   65 MET cc_start: 0.7474 (mmt) cc_final: 0.7094 (mmm)
REVERT: B   91 MET cc_start: 0.7661 (mtp) cc_final: 0.7457 (mtt)
REVERT: B  198 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7363 (mp)
REVERT: B  233 ASN cc_start: 0.7852 (m110) cc_final: 0.7417 (m110)
  outliers start: 12
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0943
  time to fit residues: 9.8692
Evaluate side-chains
  71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  319 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 66 optimal weight:    0.0980
   chunk 62 optimal weight:    0.2980
   chunk 45 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.164680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.137134 restraints weight = 7193.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.87
r_work: 0.3430 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6732  Z= 0.118
  Angle     :  0.571   8.672   9151  Z= 0.281
  Chirality :  0.042   0.149   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  4.989  27.025    934
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.33 %
    Favored  : 82.40 %
  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 aren not related in a simple way.
  whole: -1.66 (0.28), residues: 882
  helix: -0.47 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.59 (0.33), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 160 
 TYR   0.006   0.001   TYR B 255 
 PHE   0.020   0.001   PHE B  95 
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6730)
  covalent geometry    : angle       0.56389 ( 9147)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       4.43459 (    4)
  hydrogen bonds       : bond        0.02950 (  336)
  hydrogen bonds       : angle       4.11463 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7713 (mtt-85) cc_final: 0.7081 (mtm-85)
REVERT: A  147 ARG cc_start: 0.7836 (ptt-90) cc_final: 0.7415 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6769 (mtt180) cc_final: 0.5874 (mtp180)
REVERT: A  282 ARG cc_start: 0.7292 (mpt90) cc_final: 0.6854 (mtm110)
REVERT: A  294 MET cc_start: 0.7208 (ttp) cc_final: 0.6707 (ttt)
REVERT: B   65 MET cc_start: 0.7466 (mmt) cc_final: 0.7031 (mmm)
REVERT: B  198 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7351 (mp)
  outliers start: 15
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0959
  time to fit residues: 9.6427
Evaluate side-chains
  70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 74 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9980
   chunk 53 optimal weight:    0.1980
   chunk 43 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.164060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.135971 restraints weight = 7316.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.91
r_work: 0.3383 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6732  Z= 0.120
  Angle     :  0.577   9.327   9151  Z= 0.284
  Chirality :  0.042   0.146   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  4.954  26.373    934
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.78 %
    Favored  : 82.40 %
  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 aren not related in a simple way.
  whole: -1.40 (0.28), residues: 882
  helix: -0.26 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.53 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 160 
 TYR   0.006   0.001   TYR A 229 
 PHE   0.021   0.001   PHE B  95 
 TRP   0.010   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6730)
  covalent geometry    : angle       0.56641 ( 9147)
  SS BOND              : bond        0.00063 (    2)
  SS BOND              : angle       5.27641 (    4)
  hydrogen bonds       : bond        0.02939 (  336)
  hydrogen bonds       : angle       4.08608 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  126 ARG cc_start: 0.7706 (mtt-85) cc_final: 0.7084 (mtm-85)
REVERT: A  147 ARG cc_start: 0.7855 (ptt-90) cc_final: 0.7394 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6810 (mtt180) cc_final: 0.5921 (mtp180)
REVERT: A  282 ARG cc_start: 0.7394 (mpt90) cc_final: 0.6868 (mtm110)
REVERT: A  294 MET cc_start: 0.7214 (ttp) cc_final: 0.6710 (ttt)
REVERT: B   65 MET cc_start: 0.7486 (mmt) cc_final: 0.7051 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0762
  time to fit residues: 7.2974
Evaluate side-chains
  70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    0.0970
   chunk 62 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5178

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.166023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.138077 restraints weight = 7284.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 1.90
r_work: 0.3480 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6732  Z= 0.115
  Angle     :  0.580  11.648   9151  Z= 0.282
  Chirality :  0.042   0.176   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  4.911  26.672    934
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.24 %
    Favored  : 82.25 %
  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 aren not related in a simple way.
  whole: -1.19 (0.28), residues: 882
  helix: -0.09 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.51 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 147 
 TYR   0.005   0.001   TYR B  94 
 PHE   0.020   0.001   PHE B  95 
 TRP   0.009   0.001   TRP B 291 
 HIS   0.003   0.000   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6730)
  covalent geometry    : angle       0.57351 ( 9147)
  SS BOND              : bond        0.00088 (    2)
  SS BOND              : angle       4.23244 (    4)
  hydrogen bonds       : bond        0.02880 (  336)
  hydrogen bonds       : angle       4.04076 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.7058 (mtm-85)
REVERT: A  147 ARG cc_start: 0.7848 (ptt-90) cc_final: 0.7402 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6750 (mtt180) cc_final: 0.5866 (mtp180)
REVERT: A  282 ARG cc_start: 0.7368 (mpt90) cc_final: 0.6848 (mtm110)
REVERT: A  294 MET cc_start: 0.7230 (ttp) cc_final: 0.6717 (ttt)
REVERT: B   65 MET cc_start: 0.7465 (mmt) cc_final: 0.7041 (mmm)
  outliers start: 10
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0666
  time to fit residues: 6.3214
Evaluate side-chains
  69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0870
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0670
   chunk 80 optimal weight:    0.9980
   chunk 51 optimal weight:    0.2980
   chunk 74 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   overall best weight:    0.3896

-------------------------------------------------------------------------------
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 = 0.3848 r_free = 0.3848 target = 0.165943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.137940 restraints weight = 7190.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.90
r_work: 0.3487 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6732  Z= 0.106
  Angle     :  0.565  10.535   9151  Z= 0.275
  Chirality :  0.042   0.175   1084
  Planarity :  0.004   0.047   1147
  Dihedral  :  4.822  25.417    934
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.39 %
    Favored  : 82.40 %
  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 aren not related in a simple way.
  whole: -0.95 (0.28), residues: 882
  helix:  0.10 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.47 (0.34), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 147 
 TYR   0.005   0.001   TYR A 255 
 PHE   0.021   0.001   PHE B  95 
 TRP   0.008   0.001   TRP B 291 
 HIS   0.003   0.000   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6730)
  covalent geometry    : angle       0.56070 ( 9147)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       3.42569 (    4)
  hydrogen bonds       : bond        0.02816 (  336)
  hydrogen bonds       : angle       3.97908 (  999)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7041 (mtm-85)
REVERT: A  147 ARG cc_start: 0.7799 (ptt-90) cc_final: 0.7428 (ptt-90)
REVERT: A  174 ARG cc_start: 0.6746 (mtt180) cc_final: 0.5946 (mtp180)
REVERT: A  282 ARG cc_start: 0.7340 (mpt90) cc_final: 0.6865 (mtm110)
REVERT: A  294 MET cc_start: 0.7211 (ttp) cc_final: 0.6690 (ttt)
REVERT: B   65 MET cc_start: 0.7447 (mmt) cc_final: 0.7030 (mmm)
  outliers start: 8
  outliers final: 7
  residues processed: 70
  average time/residue: 0.0678
  time to fit residues: 6.3089
Evaluate side-chains
  70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain B residue   41 VAL
Chi-restraints excluded: chain B residue  283 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 7 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.165042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.137070 restraints weight = 7171.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.88
r_work: 0.3361 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6732  Z= 0.125
  Angle     :  0.582  10.645   9151  Z= 0.284
  Chirality :  0.043   0.175   1084
  Planarity :  0.004   0.048   1147
  Dihedral  :  4.871  26.192    934
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 16.69 %
    Favored  : 81.94 %
  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 aren not related in a simple way.
  whole: -0.90 (0.28), residues: 882
  helix:  0.14 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.43 (0.35), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 147 
 TYR   0.006   0.001   TYR A 255 
 PHE   0.022   0.001   PHE B  95 
 TRP   0.009   0.001   TRP B 291 
 HIS   0.003   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6730)
  covalent geometry    : angle       0.57726 ( 9147)
  SS BOND              : bond        0.00035 (    2)
  SS BOND              : angle       3.59437 (    4)
  hydrogen bonds       : bond        0.02921 (  336)
  hydrogen bonds       : angle       4.02191 (  999)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1817.86 seconds
wall clock time: 31 minutes 46.77 seconds (1906.77 seconds total)