Starting phenix.real_space_refine
on Tue Mar  3 14:59:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gah_29899/03_2026/8gah_29899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gah_29899/03_2026/8gah_29899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gah_29899/03_2026/8gah_29899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gah_29899/03_2026/8gah_29899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gah_29899/03_2026/8gah_29899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gah_29899/03_2026/8gah_29899.cif"
  }
  resolution = 2.9
  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=   0.003 sd=   0.079
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      40      5.16       5
     Cl      4      4.86       5
     C    4232      2.51       5
     N    1059      2.21       5
     O    1089      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 6424
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3205
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 412}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 3215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3215
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 412}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    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: 1.52, per 1000 atoms: 0.24
  Number of scatterers: 6424
  At special positions: 0
  Unit cell: (80.025, 107.25, 75.9, 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      40     16.00
     O    1089      8.00
     N    1059      7.00
     C    4232      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: 0.48
  Conformation dependent library (CDL) restraints added in 250.4 milliseconds
  

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 1 sheets defined
      76.2% alpha, 0.5% 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 33 through 46
      removed outlier: 3.561A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 66
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.646A  pdb=" N   ALA A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 114
    Processing helix  chain 'A' and resid 123 through 141
      Proline residue:  A 129  - end of helix
      removed outlier: 3.626A  pdb=" N   PHE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 166
    Processing helix  chain 'A' and resid 170 through 175
      removed outlier: 3.617A  pdb=" N   ARG A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 190
      removed outlier: 4.787A  pdb=" N   GLY A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   ALA A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 203
      removed outlier: 3.765A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 233
      removed outlier: 3.925A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 278
      removed outlier: 3.518A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.980A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.877A  pdb=" N   LEU A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 313
      removed outlier: 3.599A  pdb=" N   SER A 313 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 325
      removed outlier: 3.706A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 349
      removed outlier: 3.525A  pdb=" N   ILE A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 379
      removed outlier: 3.583A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
      removed outlier: 3.735A  pdb=" N   HIS A 383 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 380 through 383'
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 4.000A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 401
    Processing helix  chain 'A' and resid 404 through 416
      removed outlier: 3.520A  pdb=" N   ILE A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 440
      removed outlier: 3.637A  pdb=" N   ALA A 432 " --> pdb=" O   THR A 428 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLN A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 457
      removed outlier: 3.617A  pdb=" N   ALA A 454 " --> pdb=" O   CYS A 450 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS A 455 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 65
      removed outlier: 3.904A  pdb=" N   ILE B  35 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU B  36 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 72
    Processing helix  chain 'B' and resid 74 through 79
    Processing helix  chain 'B' and resid 79 through 100
      removed outlier: 4.033A  pdb=" N   ALA B  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU B  89 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 105
      removed outlier: 3.757A  pdb=" N   GLY B 105 " --> pdb=" O   PRO B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 113
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 3.750A  pdb=" N   VAL B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 139
      removed outlier: 3.791A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 165
      removed outlier: 4.025A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 188
      removed outlier: 3.676A  pdb=" N   LEU B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR B 180 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 203
      removed outlier: 3.829A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE B 201 " --> pdb=" O   ILE B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 233
      removed outlier: 4.195A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 252
    Processing helix  chain 'B' and resid 253 through 281
      removed outlier: 3.605A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
    Processing helix  chain 'B' and resid 287 through 305
      removed outlier: 3.502A  pdb=" N   VAL B 292 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   MET B 294 " --> pdb=" O   LYS B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 325
      removed outlier: 3.513A  pdb=" N   ALA B 325 " --> pdb=" O   PRO B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 349
      removed outlier: 3.755A  pdb=" N   LEU B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 375
      removed outlier: 3.797A  pdb=" N   VAL B 366 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 393
      removed outlier: 4.054A  pdb=" N   PHE B 389 " --> pdb=" O   GLU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 397
      removed outlier: 4.130A  pdb=" N   LEU B 397 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 394 through 397'
    Processing helix  chain 'B' and resid 404 through 413
    Processing helix  chain 'B' and resid 418 through 420
      No H-bonds generated for 'chain 'B' and resid 418 through 420'
    Processing helix  chain 'B' and resid 421 through 428
      removed outlier: 3.609A  pdb=" N   ILE B 427 " --> pdb=" O   LEU B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 440
      removed outlier: 3.664A  pdb=" N   GLY B 440 " --> pdb=" O   ALA B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 460
      removed outlier: 4.215A  pdb=" N   GLU B 459 " --> pdb=" O   LYS B 455 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLN B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211

    401 hydrogen bonds defined for protein.
    1179 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: 0.95

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1593
        1.33 -     1.45: 1215
        1.45 -     1.57: 3681
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6563
  Sorted by residual:
  bond pdb=" C   THR B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.91e+00
  bond pdb=" C   ILE B 109 "
       pdb=" N   PRO B 110 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.40e+00
  bond pdb=" CA  LEU A 136 "
       pdb=" C   LEU A 136 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.026 1.24e-02 6.50e+03 4.34e+00
  bond pdb=" C   LEU A 136 "
       pdb=" O   LEU A 136 "
    ideal  model  delta    sigma   weight residual
    1.236  1.215  0.022 1.15e-02 7.56e+03 3.52e+00
  bond pdb=" CG  LEU A 145 "
       pdb=" CD1 LEU A 145 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.94e+00
  ... (remaining 6558 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 8541
        1.87 -     3.75: 302
        3.75 -     5.62: 55
        5.62 -     7.49: 16
        7.49 -     9.37: 6
  Bond angle restraints: 8920
  Sorted by residual:
  angle pdb=" N   LEU B 163 "
        pdb=" CA  LEU B 163 "
        pdb=" C   LEU B 163 "
      ideal   model   delta    sigma   weight residual
     114.62  106.26    8.36 1.14e+00 7.69e-01 5.38e+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  122.95   -2.71 6.30e-01 2.52e+00 1.85e+01
  angle pdb=" CA  LEU B 163 "
        pdb=" C   LEU B 163 "
        pdb=" N   ASP B 164 "
      ideal   model   delta    sigma   weight residual
     119.71  114.82    4.89 1.17e+00 7.31e-01 1.75e+01
  angle pdb=" C   LEU B 413 "
        pdb=" N   GLU B 414 "
        pdb=" CA  GLU B 414 "
      ideal   model   delta    sigma   weight residual
     126.45  133.09   -6.64 1.77e+00 3.19e-01 1.41e+01
  angle pdb=" C   THR A 251 "
        pdb=" N   LEU A 252 "
        pdb=" CA  LEU A 252 "
      ideal   model   delta    sigma   weight residual
     120.60  125.76   -5.16 1.60e+00 3.91e-01 1.04e+01
  ... (remaining 8915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 3398
       17.38 -    34.76: 323
       34.76 -    52.14: 53
       52.14 -    69.51: 6
       69.51 -    86.89: 3
  Dihedral angle restraints: 3783
    sinusoidal: 1403
      harmonic: 2380
  Sorted by residual:
  dihedral pdb=" CA  VAL B 412 "
           pdb=" C   VAL B 412 "
           pdb=" N   LEU B 413 "
           pdb=" CA  LEU B 413 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.90   20.10     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CA  HIS B 284 "
           pdb=" C   HIS B 284 "
           pdb=" N   GLY B 285 "
           pdb=" CA  GLY B 285 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.76   19.24     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLU B 414 "
           pdb=" C   GLU B 414 "
           pdb=" N   MET B 415 "
           pdb=" CA  MET B 415 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.14   18.86     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 3780 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 875
       0.064 -    0.128: 166
       0.128 -    0.192: 13
       0.192 -    0.256: 1
       0.256 -    0.320: 1
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CG  LEU B 145 "
            pdb=" CB  LEU B 145 "
            pdb=" CD1 LEU B 145 "
            pdb=" CD2 LEU B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.27   -0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CB  THR A  71 "
            pdb=" CA  THR A  71 "
            pdb=" OG1 THR A  71 "
            pdb=" CG2 THR A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.30e-01
  chirality pdb=" CB  VAL B 341 "
            pdb=" CA  VAL B 341 "
            pdb=" CG1 VAL B 341 "
            pdb=" CG2 VAL B 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.14e-01
  ... (remaining 1053 not shown)

  Planarity restraints: 1116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 358 "   -0.045 5.00e-02 4.00e+02   6.70e-02 7.19e+00
        pdb=" N   PRO B 359 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 359 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 359 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 266 "    0.044 5.00e-02 4.00e+02   6.61e-02 6.99e+00
        pdb=" N   PRO B 267 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B 267 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 267 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "    0.044 5.00e-02 4.00e+02   6.59e-02 6.96e+00
        pdb=" N   PRO A 150 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1113 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1865
        2.80 -     3.33: 5669
        3.33 -     3.85: 10983
        3.85 -     4.38: 13981
        4.38 -     4.90: 22990
  Nonbonded interactions: 55488
  Sorted by model distance:
  nonbonded pdb=" O   THR B 176 "
            pdb=" OG1 THR B 180 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG  SER A 401 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OH  TYR B  94 "
            pdb=" OG  SER B 350 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   THR B 365 "
            pdb=" OG1 THR B 369 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG  SER B  86 "
            pdb=" O   GLY B 141 "
     model   vdw
     2.309 3.040
  ... (remaining 55483 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 30 through 206 or (resid 207 through 208 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 209 through 502))
}

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:             2.460
  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:             0.020
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.070
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
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   0.065   6563  Z= 0.221
  Angle     :  0.876   9.368   8920  Z= 0.472
  Chirality :  0.049   0.320   1056
  Planarity :  0.008   0.067   1116
  Dihedral  : 13.563  86.891   2283
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  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: -6.49 (0.16), residues: 860
  helix: -4.45 (0.08), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.92 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 147 
 TYR   0.014   0.002   TYR B 100 
 PHE   0.014   0.001   PHE A 357 
 TRP   0.039   0.002   TRP B 291 
 HIS   0.002   0.001   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 6563)
  covalent geometry    : angle       0.87559 ( 8920)
  hydrogen bonds       : bond        0.29260 (  401)
  hydrogen bonds       : angle      10.98367 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.7982 (mttt) cc_final: 0.7265 (pttp)
REVERT: A  410 ILE cc_start: 0.8513 (tp) cc_final: 0.8096 (mp)
REVERT: A  455 LYS cc_start: 0.7731 (tttt) cc_final: 0.7079 (ttpt)
REVERT: B   62 ASN cc_start: 0.7062 (m110) cc_final: 0.6860 (t0)
REVERT: B  117 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7699 (mt-10)
REVERT: B  282 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7404 (mtt-85)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.4768
  time to fit residues: 64.8549
Evaluate side-chains
  96 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 157 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.153615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.130642 restraints weight = 6926.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 1.48
r_work: 0.3377 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6563  Z= 0.161
  Angle     :  0.641   6.892   8920  Z= 0.329
  Chirality :  0.040   0.140   1056
  Planarity :  0.006   0.049   1116
  Dihedral  :  5.540  24.795    912
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.31 %
    Favored  : 84.89 %
  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 are not related in a simple way.
  whole: -3.30 (0.25), residues: 860
  helix: -1.97 (0.18), residues: 626
  sheet:  None (None), residues: 0
  loop : -2.26 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 126 
 TYR   0.011   0.002   TYR B 100 
 PHE   0.011   0.001   PHE A 219 
 TRP   0.020   0.001   TRP B 291 
 HIS   0.002   0.001   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6563)
  covalent geometry    : angle       0.64086 ( 8920)
  hydrogen bonds       : bond        0.04517 (  401)
  hydrogen bonds       : angle       5.11194 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.7760 (mttt) cc_final: 0.6469 (pttp)
REVERT: A  410 ILE cc_start: 0.8043 (tp) cc_final: 0.7579 (mp)
REVERT: A  455 LYS cc_start: 0.7528 (tttt) cc_final: 0.6400 (ttpt)
REVERT: B  119 GLN cc_start: 0.7901 (mt0) cc_final: 0.7291 (mm110)
REVERT: B  166 PHE cc_start: 0.7257 (m-10) cc_final: 0.6850 (m-10)
REVERT: B  391 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8039 (mp)
  outliers start: 18
  outliers final: 7
  residues processed: 120
  average time/residue: 0.4457
  time to fit residues: 56.4375
Evaluate side-chains
  106 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  398 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0870
   chunk 3 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 42 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** 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 = 0.3693 r_free = 0.3693 target = 0.152044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.129346 restraints weight = 6927.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.46
r_work: 0.3356 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
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   0.044   6563  Z= 0.145
  Angle     :  0.592   6.771   8920  Z= 0.301
  Chirality :  0.040   0.141   1056
  Planarity :  0.005   0.046   1116
  Dihedral  :  5.281  26.158    912
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 14.95 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.28), residues: 860
  helix: -0.62 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -1.96 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 147 
 TYR   0.011   0.001   TYR B 100 
 PHE   0.012   0.001   PHE A 219 
 TRP   0.019   0.001   TRP B 291 
 HIS   0.003   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6563)
  covalent geometry    : angle       0.59161 ( 8920)
  hydrogen bonds       : bond        0.03859 (  401)
  hydrogen bonds       : angle       4.41101 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7590 (mtm-85)
REVERT: A  410 ILE cc_start: 0.8061 (tp) cc_final: 0.7629 (mp)
REVERT: A  455 LYS cc_start: 0.7520 (tttt) cc_final: 0.6370 (ttpt)
REVERT: B  119 GLN cc_start: 0.7879 (mt0) cc_final: 0.7253 (mm110)
REVERT: B  166 PHE cc_start: 0.7235 (m-10) cc_final: 0.6839 (m-10)
  outliers start: 15
  outliers final: 2
  residues processed: 109
  average time/residue: 0.4795
  time to fit residues: 55.2419
Evaluate side-chains
  95 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  435 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 46 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.151805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.128945 restraints weight = 6938.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.47
r_work: 0.3314 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6563  Z= 0.154
  Angle     :  0.592   6.855   8920  Z= 0.299
  Chirality :  0.041   0.145   1056
  Planarity :  0.005   0.045   1116
  Dihedral  :  5.216  25.356    912
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.51 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.29), residues: 860
  helix: -0.13 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.01 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 147 
 TYR   0.010   0.001   TYR B 100 
 PHE   0.010   0.001   PHE A 219 
 TRP   0.011   0.001   TRP B 291 
 HIS   0.003   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 6563)
  covalent geometry    : angle       0.59183 ( 8920)
  hydrogen bonds       : bond        0.03761 (  401)
  hydrogen bonds       : angle       4.25998 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6613 (mtt90)
REVERT: A  282 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7633 (mtm-85)
REVERT: A  410 ILE cc_start: 0.8071 (tp) cc_final: 0.7713 (mp)
REVERT: A  455 LYS cc_start: 0.7458 (tttt) cc_final: 0.6321 (ttpt)
REVERT: B  119 GLN cc_start: 0.7952 (mt0) cc_final: 0.7303 (mm110)
REVERT: B  126 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7760 (mtt90)
REVERT: B  166 PHE cc_start: 0.7317 (m-10) cc_final: 0.6869 (m-10)
REVERT: B  317 PHE cc_start: 0.8526 (m-10) cc_final: 0.8300 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 109
  average time/residue: 0.4266
  time to fit residues: 49.2763
Evaluate side-chains
  106 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  398 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0980
   chunk 49 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.152228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.129327 restraints weight = 6925.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.46
r_work: 0.3339 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6563  Z= 0.130
  Angle     :  0.566   6.767   8920  Z= 0.286
  Chirality :  0.040   0.139   1056
  Planarity :  0.004   0.044   1116
  Dihedral  :  5.076  26.651    912
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.07 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.29), residues: 860
  helix:  0.19 (0.22), residues: 628
  sheet:  None (None), residues: 0
  loop : -1.91 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 147 
 TYR   0.010   0.001   TYR B 100 
 PHE   0.010   0.001   PHE A 219 
 TRP   0.005   0.001   TRP B 291 
 HIS   0.002   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6563)
  covalent geometry    : angle       0.56625 ( 8920)
  hydrogen bonds       : bond        0.03533 (  401)
  hydrogen bonds       : angle       4.07463 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6639 (mtt90)
REVERT: A  282 ARG cc_start: 0.7911 (mtp180) cc_final: 0.7693 (mtm-85)
REVERT: A  410 ILE cc_start: 0.8072 (tp) cc_final: 0.7678 (mp)
REVERT: A  455 LYS cc_start: 0.7523 (tttt) cc_final: 0.6405 (ttpt)
REVERT: B  119 GLN cc_start: 0.7934 (mt0) cc_final: 0.7302 (mm110)
REVERT: B  126 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8079 (mtt180)
REVERT: B  166 PHE cc_start: 0.7339 (m-10) cc_final: 0.6870 (m-10)
REVERT: B  317 PHE cc_start: 0.8511 (m-10) cc_final: 0.8293 (m-80)
  outliers start: 18
  outliers final: 8
  residues processed: 107
  average time/residue: 0.4624
  time to fit residues: 52.4408
Evaluate side-chains
  101 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  130 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    0.0670
   chunk 8 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.3697 r_free = 0.3697 target = 0.151987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.129113 restraints weight = 6882.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.46
r_work: 0.3314 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6563  Z= 0.147
  Angle     :  0.585   6.988   8920  Z= 0.294
  Chirality :  0.041   0.144   1056
  Planarity :  0.004   0.044   1116
  Dihedral  :  5.069  25.463    912
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.31 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.30), residues: 860
  helix:  0.32 (0.22), residues: 630
  sheet:  None (None), residues: 0
  loop : -1.88 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 147 
 TYR   0.010   0.001   TYR B 100 
 PHE   0.010   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.003   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6563)
  covalent geometry    : angle       0.58457 ( 8920)
  hydrogen bonds       : bond        0.03594 (  401)
  hydrogen bonds       : angle       4.07979 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6636 (mtt90)
REVERT: A  282 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7665 (mtm-85)
REVERT: A  410 ILE cc_start: 0.8129 (tp) cc_final: 0.7745 (mp)
REVERT: A  455 LYS cc_start: 0.7447 (tttt) cc_final: 0.6318 (ttpt)
REVERT: B  119 GLN cc_start: 0.7933 (mt0) cc_final: 0.7303 (mm110)
REVERT: B  166 PHE cc_start: 0.7364 (m-10) cc_final: 0.6909 (m-10)
  outliers start: 18
  outliers final: 10
  residues processed: 110
  average time/residue: 0.4416
  time to fit residues: 51.5279
Evaluate side-chains
  103 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  398 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 78 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 233 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.150933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.128030 restraints weight = 6851.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.44
r_work: 0.3281 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6563  Z= 0.161
  Angle     :  0.600   8.032   8920  Z= 0.301
  Chirality :  0.041   0.145   1056
  Planarity :  0.005   0.046   1116
  Dihedral  :  5.108  25.078    912
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.31 %
    Favored  : 77.41 %
  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 are not related in a simple way.
  whole: -0.39 (0.30), residues: 860
  helix:  0.36 (0.22), residues: 630
  sheet:  None (None), residues: 0
  loop : -1.83 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 126 
 TYR   0.010   0.001   TYR B 100 
 PHE   0.010   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.003   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6563)
  covalent geometry    : angle       0.60014 ( 8920)
  hydrogen bonds       : bond        0.03669 (  401)
  hydrogen bonds       : angle       4.12668 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  167 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6593 (mtt90)
REVERT: A  282 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7655 (mtm-85)
REVERT: A  403 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6978 (mtt90)
REVERT: A  410 ILE cc_start: 0.8103 (tp) cc_final: 0.7716 (mp)
REVERT: A  455 LYS cc_start: 0.7407 (tttt) cc_final: 0.6276 (ttpt)
REVERT: B  119 GLN cc_start: 0.7943 (mt0) cc_final: 0.7302 (mm110)
REVERT: B  166 PHE cc_start: 0.7298 (m-10) cc_final: 0.6820 (m-10)
REVERT: B  330 MET cc_start: 0.8039 (tpt) cc_final: 0.7631 (mmm)
  outliers start: 21
  outliers final: 11
  residues processed: 109
  average time/residue: 0.4615
  time to fit residues: 53.2174
Evaluate side-chains
  106 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  398 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0570
   chunk 10 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.151644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.128881 restraints weight = 6800.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.45
r_work: 0.3314 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6563  Z= 0.146
  Angle     :  0.597   7.266   8920  Z= 0.298
  Chirality :  0.041   0.148   1056
  Planarity :  0.005   0.047   1116
  Dihedral  :  5.057  25.463    912
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.25 %
    Favored  : 77.41 %
  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 are not related in a simple way.
  whole: -0.30 (0.29), residues: 860
  helix:  0.47 (0.22), residues: 626
  sheet:  None (None), residues: 0
  loop : -1.89 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 174 
 TYR   0.010   0.001   TYR B 100 
 PHE   0.011   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.003   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6563)
  covalent geometry    : angle       0.59712 ( 8920)
  hydrogen bonds       : bond        0.03594 (  401)
  hydrogen bonds       : angle       4.09014 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6556 (mtt90)
REVERT: A  290 LYS cc_start: 0.7886 (mtmt) cc_final: 0.7535 (mtmt)
REVERT: A  410 ILE cc_start: 0.8088 (tp) cc_final: 0.7712 (mp)
REVERT: A  455 LYS cc_start: 0.7410 (tttt) cc_final: 0.6293 (ttpt)
REVERT: B   62 ASN cc_start: 0.7010 (m110) cc_final: 0.6758 (t0)
REVERT: B  119 GLN cc_start: 0.7927 (mt0) cc_final: 0.7305 (mm110)
REVERT: B  166 PHE cc_start: 0.7314 (m-10) cc_final: 0.6831 (m-10)
REVERT: B  330 MET cc_start: 0.8029 (tpt) cc_final: 0.7606 (mmm)
  outliers start: 15
  outliers final: 11
  residues processed: 105
  average time/residue: 0.4537
  time to fit residues: 50.4186
Evaluate side-chains
  103 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  398 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.149338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.126447 restraints weight = 6977.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.44
r_work: 0.3329 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6563  Z= 0.177
  Angle     :  0.632   9.045   8920  Z= 0.314
  Chirality :  0.043   0.157   1056
  Planarity :  0.005   0.047   1116
  Dihedral  :  5.143  24.006    912
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 20.25 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.29), residues: 860
  helix:  0.36 (0.22), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.87 (0.39), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.009   0.002   TYR B 100 
 PHE   0.011   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.004   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 6563)
  covalent geometry    : angle       0.63241 ( 8920)
  hydrogen bonds       : bond        0.03762 (  401)
  hydrogen bonds       : angle       4.18381 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  167 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6655 (mtt90)
REVERT: A  174 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7462 (mtp-110)
REVERT: A  289 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7879 (m)
REVERT: A  290 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7597 (mtmt)
REVERT: A  410 ILE cc_start: 0.8111 (tp) cc_final: 0.7711 (mp)
REVERT: A  438 PHE cc_start: 0.8150 (t80) cc_final: 0.7846 (t80)
REVERT: A  455 LYS cc_start: 0.7431 (tttt) cc_final: 0.6290 (ttpt)
REVERT: B   62 ASN cc_start: 0.7025 (m110) cc_final: 0.6773 (t0)
REVERT: B  119 GLN cc_start: 0.7954 (mt0) cc_final: 0.7304 (mm110)
REVERT: B  166 PHE cc_start: 0.7361 (m-10) cc_final: 0.6912 (m-10)
REVERT: B  330 MET cc_start: 0.8051 (tpt) cc_final: 0.7693 (mmm)
  outliers start: 16
  outliers final: 10
  residues processed: 107
  average time/residue: 0.4779
  time to fit residues: 54.2663
Evaluate side-chains
  107 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  398 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 11 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 = 0.3678 r_free = 0.3678 target = 0.150419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.127639 restraints weight = 6814.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.45
r_work: 0.3308 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6563  Z= 0.164
  Angle     :  0.624   9.655   8920  Z= 0.310
  Chirality :  0.042   0.189   1056
  Planarity :  0.005   0.047   1116
  Dihedral  :  5.117  24.853    912
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 20.40 %
    Favored  : 77.41 %
  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 are not related in a simple way.
  whole: -0.30 (0.29), residues: 860
  helix:  0.43 (0.22), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.86 (0.40), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 403 
 TYR   0.009   0.001   TYR B 100 
 PHE   0.011   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.003   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 6563)
  covalent geometry    : angle       0.62392 ( 8920)
  hydrogen bonds       : bond        0.03693 (  401)
  hydrogen bonds       : angle       4.15880 ( 1179)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A  167 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6654 (mtt90)
REVERT: A  174 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7358 (mtp-110)
REVERT: A  289 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7888 (m)
REVERT: A  290 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7569 (mtmt)
REVERT: A  410 ILE cc_start: 0.8082 (tp) cc_final: 0.7691 (mp)
REVERT: A  438 PHE cc_start: 0.8125 (t80) cc_final: 0.7819 (t80)
REVERT: A  455 LYS cc_start: 0.7432 (tttt) cc_final: 0.6289 (ttpt)
REVERT: B   62 ASN cc_start: 0.7012 (m110) cc_final: 0.6767 (t0)
REVERT: B  119 GLN cc_start: 0.7936 (mt0) cc_final: 0.7305 (mm110)
REVERT: B  166 PHE cc_start: 0.7334 (m-10) cc_final: 0.6887 (m-10)
REVERT: B  330 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7683 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 102
  average time/residue: 0.4675
  time to fit residues: 50.4708
Evaluate side-chains
  105 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  398 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 46 optimal weight:    0.0970
   chunk 80 optimal weight:    2.9990
   chunk 36 optimal weight:    0.1980
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3688 r_free = 0.3688 target = 0.151326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.128540 restraints weight = 6850.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.45
r_work: 0.3306 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6563  Z= 0.147
  Angle     :  0.611  10.684   8920  Z= 0.303
  Chirality :  0.041   0.179   1056
  Planarity :  0.005   0.047   1116
  Dihedral  :  5.062  25.339    912
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 20.40 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.30), residues: 860
  helix:  0.50 (0.22), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.84 (0.40), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.009   0.001   TYR B 100 
 PHE   0.011   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.003   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6563)
  covalent geometry    : angle       0.61052 ( 8920)
  hydrogen bonds       : bond        0.03595 (  401)
  hydrogen bonds       : angle       4.10623 ( 1179)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1989.62 seconds
wall clock time: 34 minutes 32.55 seconds (2072.55 seconds total)