Starting phenix.real_space_refine
on Thu Jul  2 03:42:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gah_29899/07_2026/8gah_29899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gah_29899/07_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gah_29899/07_2026/8gah_29899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gah_29899/07_2026/8gah_29899.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gah_29899/07_2026/8gah_29899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gah_29899/07_2026/8gah_29899.map"
  }
  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-6108/lib/python3.11/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, 0
          Ad-hoc single atom residues: {' CL': 2}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 0
          Ad-hoc single atom residues: {' CL': 2}
          Chain breaks: 2
  Time building chain proxies: 1.67, per 1000 atoms: 0.26
  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: 0.40
  Conformation dependent library (CDL) restraints added in 368.2 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: 0.17
  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: 0.83

  Time building geometry restraints manager: 0.54 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:             3.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.860
  Find NCS groups from input model:        0.060
  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:6.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
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/Z
  covalent geometry    : bond        0.00517 /  0.22 ( 6563)
  covalent geometry    : angle       0.87559 /  0.47 ( 8920)
  hydrogen bonds       : bond        0.29260 / 19.16 (  401)
  hydrogen bonds       : angle      10.98367 /  7.48 ( 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  : 0.171 
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: 0.3684
  time to fit residues: 50.4653
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  : 0.239 
-------------------------------------------------------------------------------
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:    0.0870
   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:    0.4758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3726 r_free = 0.3726 target = 0.154565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.131713 restraints weight = 6922.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.48
r_work: 0.3362 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6563  Z= 0.150
  Angle     :  0.631   6.836   8920  Z= 0.325
  Chirality :  0.040   0.133   1056
  Planarity :  0.006   0.048   1116
  Dihedral  :  5.510  25.432    912
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 12.31 %
    Favored  : 85.05 %
  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: -3.27 (0.25), residues: 860
  helix: -1.94 (0.18), residues: 626
  sheet:  None (None), residues: 0
  loop : -2.27 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 126 
 TYR   0.010   0.001   TYR B 100 
 PHE   0.011   0.001   PHE A 219 
 TRP   0.018   0.001   TRP B 291 
 HIS   0.002   0.000   HIS B 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 ( 6563)
  covalent geometry    : angle       0.63067 /  0.33 ( 8920)
  hydrogen bonds       : bond        0.04350 /  2.87 (  401)
  hydrogen bonds       : angle       5.03930 /  3.52 ( 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
  133 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.7710 (mttt) cc_final: 0.6457 (pttp)
REVERT: A  410 ILE cc_start: 0.8026 (tp) cc_final: 0.7615 (mp)
REVERT: A  455 LYS cc_start: 0.7510 (tttt) cc_final: 0.6410 (ttpt)
REVERT: B  119 GLN cc_start: 0.7883 (mt0) cc_final: 0.7277 (mm110)
REVERT: B  166 PHE cc_start: 0.7244 (m-10) cc_final: 0.6851 (m-10)
  outliers start: 17
  outliers final: 7
  residues processed: 124
  average time/residue: 0.4165
  time to fit residues: 54.8871
Evaluate side-chains
  110 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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  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:    0.0020
   chunk 3 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3679 r_free = 0.3679 target = 0.150743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.128036 restraints weight = 6946.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.46
r_work: 0.3326 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6563  Z= 0.163
  Angle     :  0.612   7.059   8920  Z= 0.310
  Chirality :  0.041   0.147   1056
  Planarity :  0.005   0.046   1116
  Dihedral  :  5.335  25.240    912
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.95 %
    Favored  : 82.24 %
  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: 624
  sheet:  None (None), residues: 0
  loop : -1.94 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 147 
 TYR   0.011   0.002   TYR B 100 
 PHE   0.013   0.001   PHE A 219 
 TRP   0.022   0.001   TRP B 291 
 HIS   0.003   0.000   HIS B 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.16 ( 6563)
  covalent geometry    : angle       0.61190 /  0.31 ( 8920)
  hydrogen bonds       : bond        0.03975 /  2.63 (  401)
  hydrogen bonds       : angle       4.45976 /  3.13 ( 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
  117 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6581 (mtt90)
REVERT: A  282 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7636 (mtm-85)
REVERT: A  410 ILE cc_start: 0.8092 (tp) cc_final: 0.7670 (mp)
REVERT: A  455 LYS cc_start: 0.7527 (tttt) cc_final: 0.6382 (ttpt)
REVERT: B  119 GLN cc_start: 0.7952 (mt0) cc_final: 0.7291 (mm110)
REVERT: B  166 PHE cc_start: 0.7291 (m-10) cc_final: 0.6902 (m-10)
REVERT: B  377 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7985 (pt0)
  outliers start: 18
  outliers final: 4
  residues processed: 108
  average time/residue: 0.4657
  time to fit residues: 53.3362
Evaluate side-chains
  100 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  223 ILE
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  377 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 60 optimal weight:    0.0050
   chunk 24 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0170
   chunk 46 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.4632

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3696 r_free = 0.3696 target = 0.152231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.129568 restraints weight = 6936.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.45
r_work: 0.3343 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6563  Z= 0.134
  Angle     :  0.570   6.683   8920  Z= 0.288
  Chirality :  0.040   0.138   1056
  Planarity :  0.005   0.044   1116
  Dihedral  :  5.162  26.531    912
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.98 %
    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: -0.92 (0.29), residues: 860
  helix: -0.03 (0.22), residues: 620
  sheet:  None (None), residues: 0
  loop : -1.92 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 147 
 TYR   0.009   0.001   TYR B 100 
 PHE   0.010   0.001   PHE A 219 
 TRP   0.009   0.001   TRP B 291 
 HIS   0.002   0.000   HIS B 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.13 ( 6563)
  covalent geometry    : angle       0.56957 /  0.29 ( 8920)
  hydrogen bonds       : bond        0.03612 /  2.39 (  401)
  hydrogen bonds       : angle       4.19800 /  2.95 ( 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
  116 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 ASN cc_start: 0.8724 (m110) cc_final: 0.8476 (m-40)
REVERT: A  410 ILE cc_start: 0.8072 (tp) cc_final: 0.7722 (mp)
REVERT: A  455 LYS cc_start: 0.7491 (tttt) cc_final: 0.6364 (ttpt)
REVERT: B  119 GLN cc_start: 0.7934 (mt0) cc_final: 0.7299 (mm110)
REVERT: B  126 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7758 (mtt90)
REVERT: B  166 PHE cc_start: 0.7259 (m-10) cc_final: 0.6826 (m-10)
REVERT: B  317 PHE cc_start: 0.8519 (m-10) cc_final: 0.8294 (m-80)
REVERT: B  377 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7931 (pt0)
  outliers start: 16
  outliers final: 8
  residues processed: 113
  average time/residue: 0.4417
  time to fit residues: 52.7303
Evaluate side-chains
  104 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  435 LEU
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  377 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    0.0010
   chunk 73 optimal weight:    0.2980
   chunk 58 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 418 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.152124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.129411 restraints weight = 6946.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.45
r_work: 0.3338 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6563  Z= 0.133
  Angle     :  0.570   6.709   8920  Z= 0.288
  Chirality :  0.040   0.140   1056
  Planarity :  0.004   0.044   1116
  Dihedral  :  5.067  26.194    912
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.76 %
    Favored  : 78.82 %
  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: -0.52 (0.30), residues: 860
  helix:  0.26 (0.22), residues: 620
  sheet:  None (None), residues: 0
  loop : -1.77 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 147 
 TYR   0.009   0.001   TYR B 100 
 PHE   0.010   0.001   PHE A 219 
 TRP   0.006   0.001   TRP B 291 
 HIS   0.003   0.000   HIS B 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.13 ( 6563)
  covalent geometry    : angle       0.56990 /  0.29 ( 8920)
  hydrogen bonds       : bond        0.03554 /  2.34 (  401)
  hydrogen bonds       : angle       4.07997 /  2.86 ( 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
  114 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A  410 ILE cc_start: 0.8088 (tp) cc_final: 0.7721 (mp)
REVERT: A  455 LYS cc_start: 0.7534 (tttt) cc_final: 0.6413 (ttpt)
REVERT: B  119 GLN cc_start: 0.7933 (mt0) cc_final: 0.7309 (mm110)
REVERT: B  126 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8084 (mtt180)
REVERT: B  166 PHE cc_start: 0.7319 (m-10) cc_final: 0.6873 (m-10)
REVERT: B  317 PHE cc_start: 0.8521 (m-10) cc_final: 0.8300 (m-80)
REVERT: B  377 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7923 (pt0)
  outliers start: 22
  outliers final: 11
  residues processed: 109
  average time/residue: 0.4922
  time to fit residues: 56.7496
Evaluate side-chains
  105 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  289 THR
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  130 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  377 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.150248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.127407 restraints weight = 6933.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.45
r_work: 0.3314 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2543

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     :  0.597   7.143   8920  Z= 0.300
  Chirality :  0.041   0.148   1056
  Planarity :  0.005   0.045   1116
  Dihedral  :  5.122  24.737    912
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.69 %
    Favored  : 78.19 %
  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 (0.30), residues: 860
  helix:  0.34 (0.22), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.65 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 147 
 TYR   0.009   0.001   TYR A 255 
 PHE   0.011   0.001   PHE A 219 
 TRP   0.006   0.001   TRP B 291 
 HIS   0.003   0.000   HIS B 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.16 ( 6563)
  covalent geometry    : angle       0.59688 /  0.30 ( 8920)
  hydrogen bonds       : bond        0.03682 /  2.44 (  401)
  hydrogen bonds       : angle       4.13019 /  2.90 ( 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
  121 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6562 (mtt90)
REVERT: A  174 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7396 (mtp-110)
REVERT: A  410 ILE cc_start: 0.8092 (tp) cc_final: 0.7719 (mp)
REVERT: A  455 LYS cc_start: 0.7464 (tttt) cc_final: 0.6338 (ttpt)
REVERT: B   62 ASN cc_start: 0.6963 (m110) cc_final: 0.6708 (t0)
REVERT: B  119 GLN cc_start: 0.7950 (mt0) cc_final: 0.7311 (mm110)
REVERT: B  166 PHE cc_start: 0.7324 (m-10) cc_final: 0.6811 (m-10)
REVERT: B  330 MET cc_start: 0.8051 (tpt) cc_final: 0.7626 (mmm)
REVERT: B  377 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7920 (pt0)
  outliers start: 20
  outliers final: 11
  residues processed: 115
  average time/residue: 0.4536
  time to fit residues: 55.2560
Evaluate side-chains
  109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
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  289 THR
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  403 ARG
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  377 GLU
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:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    0.1980
   chunk 2 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0980
   chunk 64 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 233 ASN
B 191 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.151583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.128943 restraints weight = 6891.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.45
r_work: 0.3347 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6563  Z= 0.136
  Angle     :  0.584   7.742   8920  Z= 0.292
  Chirality :  0.040   0.145   1056
  Planarity :  0.004   0.045   1116
  Dihedral  :  5.034  26.209    912
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.40 %
    Favored  : 76.79 %
  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: -0.26 (0.30), residues: 860
  helix:  0.50 (0.22), residues: 622
  sheet:  None (None), residues: 0
  loop : -1.85 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 126 
 TYR   0.008   0.001   TYR B 100 
 PHE   0.009   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.002   0.000   HIS B 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 6563)
  covalent geometry    : angle       0.58429 /  0.29 ( 8920)
  hydrogen bonds       : bond        0.03522 /  2.33 (  401)
  hydrogen bonds       : angle       4.04505 /  2.84 ( 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
  111 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  410 ILE cc_start: 0.8091 (tp) cc_final: 0.7713 (mp)
REVERT: A  455 LYS cc_start: 0.7395 (tttt) cc_final: 0.6269 (ttpt)
REVERT: B  119 GLN cc_start: 0.7919 (mt0) cc_final: 0.7299 (mm110)
REVERT: B  162 VAL cc_start: 0.7015 (t) cc_final: 0.6760 (t)
REVERT: B  166 PHE cc_start: 0.7295 (m-10) cc_final: 0.6818 (m-10)
REVERT: B  330 MET cc_start: 0.8034 (tpt) cc_final: 0.7591 (mmm)
REVERT: B  377 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7917 (pt0)
  outliers start: 18
  outliers final: 11
  residues processed: 105
  average time/residue: 0.4389
  time to fit residues: 48.8398
Evaluate side-chains
  102 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  377 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0170
   chunk 52 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.4618

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.151895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.129374 restraints weight = 6833.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.43
r_work: 0.3340 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6563  Z= 0.133
  Angle     :  0.576   6.978   8920  Z= 0.289
  Chirality :  0.040   0.144   1056
  Planarity :  0.004   0.046   1116
  Dihedral  :  4.987  25.959    912
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.72 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.16 (0.30), residues: 860
  helix:  0.61 (0.22), residues: 620
  sheet:  None (None), residues: 0
  loop : -1.89 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.008   0.001   TYR B 100 
 PHE   0.009   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.002   0.000   HIS B 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.13 ( 6563)
  covalent geometry    : angle       0.57643 /  0.29 ( 8920)
  hydrogen bonds       : bond        0.03486 /  2.30 (  401)
  hydrogen bonds       : angle       4.03144 /  2.83 ( 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
  109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  290 LYS cc_start: 0.7868 (mtmt) cc_final: 0.7520 (mtmt)
REVERT: A  403 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6959 (mtt90)
REVERT: A  410 ILE cc_start: 0.8097 (tp) cc_final: 0.7719 (mp)
REVERT: A  455 LYS cc_start: 0.7376 (tttt) cc_final: 0.6276 (ttpt)
REVERT: B   62 ASN cc_start: 0.7003 (m110) cc_final: 0.6762 (t0)
REVERT: B  119 GLN cc_start: 0.7911 (mt0) cc_final: 0.7298 (mm110)
REVERT: B  162 VAL cc_start: 0.6992 (t) cc_final: 0.6685 (t)
REVERT: B  166 PHE cc_start: 0.7284 (m-10) cc_final: 0.6815 (m-10)
REVERT: B  330 MET cc_start: 0.8009 (tpt) cc_final: 0.7557 (mmm)
REVERT: B  377 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7907 (pt0)
  outliers start: 15
  outliers final: 9
  residues processed: 105
  average time/residue: 0.4651
  time to fit residues: 51.6566
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  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  377 GLU
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:    0.3980
   chunk 8 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0040
   chunk 11 optimal weight:    0.5980
   chunk 75 optimal weight:    0.4980
   chunk 80 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.3792

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.152863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.130117 restraints weight = 6953.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.46
r_work: 0.3390 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6563  Z= 0.124
  Angle     :  0.571   7.761   8920  Z= 0.285
  Chirality :  0.040   0.147   1056
  Planarity :  0.004   0.047   1116
  Dihedral  :  4.920  26.370    912
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 21.50 %
    Favored  : 76.79 %
  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:  0.01 (0.30), residues: 860
  helix:  0.69 (0.22), residues: 622
  sheet:  None (None), residues: 0
  loop : -1.71 (0.41), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 126 
 TYR   0.008   0.001   TYR B 100 
 PHE   0.012   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.002   0.000   HIS B 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.12 ( 6563)
  covalent geometry    : angle       0.57145 /  0.29 ( 8920)
  hydrogen bonds       : bond        0.03399 /  2.23 (  401)
  hydrogen bonds       : angle       3.97845 /  2.80 ( 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
  104 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  271 LYS cc_start: 0.8084 (mttt) cc_final: 0.6891 (mmtt)
REVERT: A  290 LYS cc_start: 0.7820 (mtmt) cc_final: 0.7474 (mtmt)
REVERT: A  403 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6894 (mtt90)
REVERT: A  410 ILE cc_start: 0.8091 (tp) cc_final: 0.7709 (mp)
REVERT: A  455 LYS cc_start: 0.7448 (tttt) cc_final: 0.6366 (ttpt)
REVERT: B   62 ASN cc_start: 0.6979 (m110) cc_final: 0.6707 (t0)
REVERT: B  119 GLN cc_start: 0.7899 (mt0) cc_final: 0.7286 (mm110)
REVERT: B  162 VAL cc_start: 0.6950 (t) cc_final: 0.6676 (t)
REVERT: B  166 PHE cc_start: 0.7245 (m-10) cc_final: 0.6768 (m-10)
REVERT: B  330 MET cc_start: 0.7960 (tpt) cc_final: 0.7534 (mmm)
REVERT: B  377 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7905 (pt0)
  outliers start: 11
  outliers final: 9
  residues processed: 100
  average time/residue: 0.4931
  time to fit residues: 52.1620
Evaluate side-chains
  102 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  377 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 1 optimal weight:    0.4980
   chunk 71 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 76 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.151272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.128590 restraints weight = 6842.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.45
r_work: 0.3342 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2752

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= 0.149
  Angle     :  0.600   9.481   8920  Z= 0.298
  Chirality :  0.042   0.149   1056
  Planarity :  0.004   0.046   1116
  Dihedral  :  4.980  24.964    912
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 21.03 %
    Favored  : 76.64 %
  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: -0.17 (0.30), residues: 860
  helix:  0.59 (0.22), residues: 630
  sheet:  None (None), residues: 0
  loop : -1.98 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.008   0.001   TYR B 100 
 PHE   0.012   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/Z
  covalent geometry    : bond        0.00355 /  0.15 ( 6563)
  covalent geometry    : angle       0.60002 /  0.30 ( 8920)
  hydrogen bonds       : bond        0.03553 /  2.34 (  401)
  hydrogen bonds       : angle       4.04410 /  2.85 ( 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
  110 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  289 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7886 (m)
REVERT: A  290 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7526 (mtmt)
REVERT: A  403 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6950 (mtt90)
REVERT: A  410 ILE cc_start: 0.8102 (tp) cc_final: 0.7718 (mp)
REVERT: A  455 LYS cc_start: 0.7464 (tttt) cc_final: 0.6344 (ttpt)
REVERT: B   62 ASN cc_start: 0.7011 (m110) cc_final: 0.6731 (t0)
REVERT: B  119 GLN cc_start: 0.7931 (mt0) cc_final: 0.7305 (mm110)
REVERT: B  166 PHE cc_start: 0.7317 (m-10) cc_final: 0.6844 (m-10)
REVERT: B  330 MET cc_start: 0.7978 (tpt) cc_final: 0.7587 (mmm)
REVERT: B  377 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7907 (pt0)
  outliers start: 15
  outliers final: 9
  residues processed: 105
  average time/residue: 0.4546
  time to fit residues: 50.4563
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  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  377 GLU
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:    0.0060
   chunk 80 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.4796

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.152845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.130303 restraints weight = 6834.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.44
r_work: 0.3342 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6563  Z= 0.137
  Angle     :  0.592  10.450   8920  Z= 0.294
  Chirality :  0.041   0.149   1056
  Planarity :  0.004   0.047   1116
  Dihedral  :  4.952  25.763    912
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 20.87 %
    Favored  : 77.10 %
  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: -0.12 (0.30), residues: 860
  helix:  0.63 (0.22), residues: 630
  sheet:  None (None), residues: 0
  loop : -1.96 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 126 
 TYR   0.008   0.001   TYR B 100 
 PHE   0.012   0.001   PHE A 219 
 TRP   0.004   0.001   TRP A  59 
 HIS   0.002   0.000   HIS B 284 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 6563)
  covalent geometry    : angle       0.59216 /  0.29 ( 8920)
  hydrogen bonds       : bond        0.03488 /  2.29 (  401)
  hydrogen bonds       : angle       4.02502 /  2.84 ( 1179)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1977.67 seconds
wall clock time: 34 minutes 25.73 seconds (2065.73 seconds total)