Starting phenix.real_space_refine
on Tue Mar  3 15:00:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w6k_32328/03_2026/7w6k_32328.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w6k_32328/03_2026/7w6k_32328.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w6k_32328/03_2026/7w6k_32328.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w6k_32328/03_2026/7w6k_32328.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w6k_32328/03_2026/7w6k_32328.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w6k_32328/03_2026/7w6k_32328.cif"
  }
  resolution = 3.5
  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=   0.002 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    4202      2.51       5
     N    1094      2.21       5
     O    1142      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 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: 6468
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 410, 3234
          Classifications: {'peptide': 410}
          Link IDs: {'PTRANS': 14, 'TRANS': 395}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.01, per 1000 atoms: 0.31
  Number of scatterers: 6468
  At special positions: 0
  Unit cell: (74.88, 92.56, 107.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1142      8.00
     N    1094      7.00
     C    4202      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: 0.61
  Conformation dependent library (CDL) restraints added in 358.3 milliseconds
  

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 0 sheets defined
      82.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 54
      removed outlier: 4.668A  pdb=" N   ASN A  41 " --> pdb=" O   MET A  37 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TRP A  44 " --> pdb=" O   PRO A  40 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLN A  45 " --> pdb=" O   ASN A  41 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A  50 " --> pdb=" O   THR A  46 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 73
    Processing helix  chain 'A' and resid 73 through 78
      removed outlier: 3.578A  pdb=" N   LEU A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 73 through 78'
    Processing helix  chain 'A' and resid 80 through 86
      removed outlier: 4.036A  pdb=" N   ILE A  84 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   GLY A  85 " --> pdb=" O   LYS A  82 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   GLN A  86 " --> pdb=" O   GLY A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 99
      removed outlier: 4.137A  pdb=" N   ALA A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 131
      removed outlier: 4.097A  pdb=" N   GLY A 110 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 160
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 4.614A  pdb=" N   LYS A 165 " --> pdb=" O   PRO A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 188
      removed outlier: 3.632A  pdb=" N   PHE A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   TYR A 186 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ARG A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A 188 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 215
      removed outlier: 3.864A  pdb=" N   LYS A 193 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   TYR A 200 " --> pdb=" O   HIS A 196 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   THR A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 249
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 263 through 288
      removed outlier: 4.775A  pdb=" N   ALA A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   VAL A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   LYS A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   SER A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ILE A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 325
    Processing helix  chain 'A' and resid 332 through 338
      removed outlier: 3.911A  pdb=" N   MET A 338 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 363
      removed outlier: 3.776A  pdb=" N   ILE A 344 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 389
    Processing helix  chain 'A' and resid 459 through 468
      removed outlier: 3.812A  pdb=" N   ILE A 463 " --> pdb=" O   GLN A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 504
      removed outlier: 4.012A  pdb=" N   ASP A 491 " --> pdb=" O   VAL A 487 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 54
      removed outlier: 4.668A  pdb=" N   ASN B  41 " --> pdb=" O   MET B  37 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TRP B  44 " --> pdb=" O   PRO B  40 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLN B  45 " --> pdb=" O   ASN B  41 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL B  50 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 73
    Processing helix  chain 'B' and resid 73 through 78
      removed outlier: 3.578A  pdb=" N   LEU B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU B  78 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 73 through 78'
    Processing helix  chain 'B' and resid 80 through 86
      removed outlier: 4.037A  pdb=" N   ILE B  84 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   GLY B  85 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   GLN B  86 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 99
      removed outlier: 4.137A  pdb=" N   ALA B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 131
      removed outlier: 4.096A  pdb=" N   GLY B 110 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 160
    Processing helix  chain 'B' and resid 160 through 165
      removed outlier: 4.614A  pdb=" N   LYS B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 188
      removed outlier: 3.632A  pdb=" N   PHE B 174 " --> pdb=" O   GLY B 170 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   TYR B 186 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ARG B 187 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU B 188 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 215
      removed outlier: 3.864A  pdb=" N   LYS B 193 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   TYR B 200 " --> pdb=" O   HIS B 196 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   THR B 201 " --> pdb=" O   ASP B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 249
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 263 through 288
      removed outlier: 4.775A  pdb=" N   ALA B 271 " --> pdb=" O   LYS B 267 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   VAL B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   LYS B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ILE B 278 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 325
    Processing helix  chain 'B' and resid 332 through 338
      removed outlier: 3.910A  pdb=" N   MET B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 363
      removed outlier: 3.776A  pdb=" N   ILE B 344 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ARG B 345 " --> pdb=" O   ASP B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 389
    Processing helix  chain 'B' and resid 459 through 468
      removed outlier: 3.812A  pdb=" N   ILE B 463 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 504
      removed outlier: 4.012A  pdb=" N   ASP B 491 " --> pdb=" O   VAL B 487 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU B 492 " --> pdb=" O   ALA B 488 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1386 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.82 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: 1300
        1.33 -     1.45: 1511
        1.45 -     1.57: 3755
        1.57 -     1.69: 0
        1.69 -     1.82: 42
  Bond restraints: 6608
  Sorted by residual:
  bond pdb=" CA  SER B 358 "
       pdb=" CB  SER B 358 "
    ideal  model  delta    sigma   weight residual
    1.528  1.466  0.063 1.56e-02 4.11e+03 1.62e+01
  bond pdb=" CA  SER A 358 "
       pdb=" CB  SER A 358 "
    ideal  model  delta    sigma   weight residual
    1.528  1.466  0.063 1.56e-02 4.11e+03 1.61e+01
  bond pdb=" CA  SER B 360 "
       pdb=" CB  SER B 360 "
    ideal  model  delta    sigma   weight residual
    1.529  1.470  0.059 1.58e-02 4.01e+03 1.40e+01
  bond pdb=" N   PRO A 369 "
       pdb=" CD  PRO A 369 "
    ideal  model  delta    sigma   weight residual
    1.473  1.525 -0.052 1.40e-02 5.10e+03 1.39e+01
  bond pdb=" N   PRO B 369 "
       pdb=" CD  PRO B 369 "
    ideal  model  delta    sigma   weight residual
    1.473  1.525 -0.052 1.40e-02 5.10e+03 1.39e+01
  ... (remaining 6603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 8196
        1.85 -     3.70: 581
        3.70 -     5.54: 143
        5.54 -     7.39: 32
        7.39 -     9.24: 10
  Bond angle restraints: 8962
  Sorted by residual:
  angle pdb=" N   ILE B 252 "
        pdb=" CA  ILE B 252 "
        pdb=" C   ILE B 252 "
      ideal   model   delta    sigma   weight residual
     108.35   99.46    8.89 1.32e+00 5.74e-01 4.54e+01
  angle pdb=" N   ILE A 252 "
        pdb=" CA  ILE A 252 "
        pdb=" C   ILE A 252 "
      ideal   model   delta    sigma   weight residual
     108.35   99.46    8.89 1.32e+00 5.74e-01 4.53e+01
  angle pdb=" N   PHE B 470 "
        pdb=" CA  PHE B 470 "
        pdb=" C   PHE B 470 "
      ideal   model   delta    sigma   weight residual
     110.23  100.99    9.24 1.45e+00 4.76e-01 4.06e+01
  angle pdb=" N   PHE A 470 "
        pdb=" CA  PHE A 470 "
        pdb=" C   PHE A 470 "
      ideal   model   delta    sigma   weight residual
     110.23  100.99    9.24 1.45e+00 4.76e-01 4.06e+01
  angle pdb=" N   GLY A 114 "
        pdb=" CA  GLY A 114 "
        pdb=" C   GLY A 114 "
      ideal   model   delta    sigma   weight residual
     112.50  119.17   -6.67 1.16e+00 7.43e-01 3.30e+01
  ... (remaining 8957 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 3484
       17.73 -    35.45: 374
       35.45 -    53.18: 68
       53.18 -    70.90: 6
       70.90 -    88.63: 4
  Dihedral angle restraints: 3936
    sinusoidal: 1542
      harmonic: 2394
  Sorted by residual:
  dihedral pdb=" C   PHE B 248 "
           pdb=" N   PHE B 248 "
           pdb=" CA  PHE B 248 "
           pdb=" CB  PHE B 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.88   12.28     0      2.50e+00 1.60e-01 2.41e+01
  dihedral pdb=" C   PHE A 248 "
           pdb=" N   PHE A 248 "
           pdb=" CA  PHE A 248 "
           pdb=" CB  PHE A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.86   12.26     0      2.50e+00 1.60e-01 2.40e+01
  dihedral pdb=" C   TYR A 257 "
           pdb=" N   TYR A 257 "
           pdb=" CA  TYR A 257 "
           pdb=" CB  TYR A 257 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.00   11.40     0      2.50e+00 1.60e-01 2.08e+01
  ... (remaining 3933 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 924
       0.086 -    0.172: 78
       0.172 -    0.259: 30
       0.259 -    0.345: 8
       0.345 -    0.431: 4
  Chirality restraints: 1044
  Sorted by residual:
  chirality pdb=" CA  PHE B 248 "
            pdb=" N   PHE B 248 "
            pdb=" C   PHE B 248 "
            pdb=" CB  PHE B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.64e+00
  chirality pdb=" CA  PHE A 248 "
            pdb=" N   PHE A 248 "
            pdb=" C   PHE A 248 "
            pdb=" CB  PHE A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.64e+00
  chirality pdb=" CA  TYR A 257 "
            pdb=" N   TYR A 257 "
            pdb=" C   TYR A 257 "
            pdb=" CB  TYR A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.04e+00
  ... (remaining 1041 not shown)

  Planarity restraints: 1112
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 161 "    0.020 2.00e-02 2.50e+03   4.07e-02 1.65e+01
        pdb=" C   PRO A 161 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PRO A 161 "    0.026 2.00e-02 2.50e+03
        pdb=" N   TYR A 162 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 161 "    0.020 2.00e-02 2.50e+03   4.06e-02 1.65e+01
        pdb=" C   PRO B 161 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   PRO B 161 "    0.026 2.00e-02 2.50e+03
        pdb=" N   TYR B 162 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 163 "   -0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   ILE B 163 "    0.063 2.00e-02 2.50e+03
        pdb=" O   ILE B 163 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LYS B 164 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1109 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2519
        2.85 -     3.36: 7355
        3.36 -     3.87: 10787
        3.87 -     4.39: 12544
        4.39 -     4.90: 19461
  Nonbonded interactions: 52666
  Sorted by model distance:
  nonbonded pdb=" N   SER A 221 "
            pdb=" OE2 GLU A 289 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" N   SER B 221 "
            pdb=" OE2 GLU B 289 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" OD1 ASP A 135 "
            pdb=" OG  SER A 138 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" OD1 ASP B 135 "
            pdb=" OG  SER B 138 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" NZ  LYS B 232 "
            pdb=" OD1 ASP B 279 "
     model   vdw
     2.366 3.120
  ... (remaining 52661 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.670
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
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      :  0.007   0.063   6608  Z= 0.485
  Angle     :  1.134   9.238   8962  Z= 0.794
  Chirality :  0.069   0.431   1044
  Planarity :  0.006   0.041   1112
  Dihedral  : 14.610  88.630   2392
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 47.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.06 %
    Favored  : 87.93 %
  Cbeta Deviations :  0.52 %
  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: -3.58 (0.24), residues: 812
  helix: -1.77 (0.18), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.84 (0.34), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 365 
 TYR   0.020   0.002   TYR A 247 
 PHE   0.040   0.003   PHE A 248 
 TRP   0.012   0.002   TRP A  44 
 HIS   0.010   0.002   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00737 ( 6608)
  covalent geometry    : angle       1.13364 ( 8962)
  hydrogen bonds       : bond        0.14333 (  466)
  hydrogen bonds       : angle       6.64181 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 175
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 PHE cc_start: 0.8116 (t80) cc_final: 0.7915 (t80)
REVERT: B   77 LEU cc_start: 0.8760 (pp) cc_final: 0.8544 (tt)
  outliers start: 14
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0850
  time to fit residues: 20.8231
Evaluate side-chains
  110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 132 ASN
A 179 ASN
A 219 ASN
A 330 GLN
A 377 HIS
A 384 ASN
A 390 GLN
B  86 GLN
B 132 ASN
B 219 ASN
B 330 GLN
B 377 HIS
B 390 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.096261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.072902 restraints weight = 19455.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.076115 restraints weight = 10300.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.078299 restraints weight = 6845.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.079637 restraints weight = 5179.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.080630 restraints weight = 4313.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   6608  Z= 0.210
  Angle     :  0.830   8.471   8962  Z= 0.422
  Chirality :  0.045   0.237   1044
  Planarity :  0.005   0.045   1112
  Dihedral  :  5.405  21.560    896
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 19.40 %
    Favored  : 76.44 %
  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: -1.65 (0.27), residues: 812
  helix: -0.55 (0.19), residues: 628
  sheet:  None (None), residues: 0
  loop : -2.60 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 502 
 TYR   0.024   0.002   TYR A 269 
 PHE   0.026   0.002   PHE A 476 
 TRP   0.017   0.002   TRP B  44 
 HIS   0.014   0.002   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 6608)
  covalent geometry    : angle       0.82978 ( 8962)
  hydrogen bonds       : bond        0.05399 (  466)
  hydrogen bonds       : angle       4.93782 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 135
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9172 (t80)
REVERT: A  169 TYR cc_start: 0.7606 (m-80) cc_final: 0.7319 (m-10)
REVERT: A  243 CYS cc_start: 0.8802 (t) cc_final: 0.8336 (t)
REVERT: A  280 GLU cc_start: 0.9524 (tp30) cc_final: 0.9222 (mt-10)
REVERT: A  375 HIS cc_start: 0.9513 (m90) cc_final: 0.9020 (m90)
REVERT: A  470 PHE cc_start: 0.8518 (m-10) cc_final: 0.8302 (m-80)
REVERT: B  125 PHE cc_start: 0.9513 (OUTLIER) cc_final: 0.9231 (t80)
REVERT: B  258 MET cc_start: 0.8599 (ptp) cc_final: 0.8386 (ptt)
REVERT: B  279 ASP cc_start: 0.8777 (m-30) cc_final: 0.8228 (t70)
REVERT: B  280 GLU cc_start: 0.9486 (tp30) cc_final: 0.9169 (mt-10)
REVERT: B  375 HIS cc_start: 0.9457 (m90) cc_final: 0.9016 (m90)
REVERT: B  485 GLU cc_start: 0.8838 (tp30) cc_final: 0.8553 (tm-30)
  outliers start: 29
  outliers final: 16
  residues processed: 155
  average time/residue: 0.0559
  time to fit residues: 12.7748
Evaluate side-chains
  122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue  125 PHE
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  494 ILE
Chi-restraints excluded: chain B residue  505 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 35 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
B 330 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.092586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.069390 restraints weight = 18700.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.072305 restraints weight = 9821.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.073991 restraints weight = 6554.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.075674 restraints weight = 5198.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.076639 restraints weight = 4262.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6608  Z= 0.174
  Angle     :  0.700   9.762   8962  Z= 0.356
  Chirality :  0.043   0.213   1044
  Planarity :  0.005   0.034   1112
  Dihedral  :  5.061  22.359    896
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 16.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 20.40 %
    Favored  : 73.99 %
  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: -0.48 (0.29), residues: 812
  helix:  0.23 (0.19), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.11 (0.50), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 291 
 TYR   0.025   0.002   TYR A  75 
 PHE   0.030   0.002   PHE A 248 
 TRP   0.011   0.002   TRP B  44 
 HIS   0.015   0.002   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6608)
  covalent geometry    : angle       0.70008 ( 8962)
  hydrogen bonds       : bond        0.04673 (  466)
  hydrogen bonds       : angle       4.57286 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.7385 (mpp) cc_final: 0.7138 (pmm)
REVERT: A  102 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8351 (t)
REVERT: A  125 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.9216 (t80)
REVERT: A  279 ASP cc_start: 0.8881 (m-30) cc_final: 0.8122 (t70)
REVERT: A  280 GLU cc_start: 0.9479 (tp30) cc_final: 0.9141 (mt-10)
REVERT: A  303 GLN cc_start: 0.8327 (tp40) cc_final: 0.7955 (mm110)
REVERT: A  375 HIS cc_start: 0.9517 (m90) cc_final: 0.9022 (m90)
REVERT: A  381 GLN cc_start: 0.8781 (mt0) cc_final: 0.8375 (mt0)
REVERT: B   37 MET cc_start: 0.7691 (mpp) cc_final: 0.7487 (pmm)
REVERT: B   45 GLN cc_start: 0.9335 (mm110) cc_final: 0.9109 (mp10)
REVERT: B   77 LEU cc_start: 0.9459 (mm) cc_final: 0.9127 (pp)
REVERT: B  239 SER cc_start: 0.9694 (m) cc_final: 0.9427 (p)
REVERT: B  243 CYS cc_start: 0.9375 (t) cc_final: 0.9025 (t)
REVERT: B  279 ASP cc_start: 0.8827 (m-30) cc_final: 0.8556 (t70)
REVERT: B  280 GLU cc_start: 0.9391 (tp30) cc_final: 0.9178 (mt-10)
REVERT: B  375 HIS cc_start: 0.9461 (m90) cc_final: 0.8997 (m90)
REVERT: B  486 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8711 (m)
  outliers start: 39
  outliers final: 20
  residues processed: 142
  average time/residue: 0.0566
  time to fit residues: 11.6779
Evaluate side-chains
  120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  262 GLU
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  327 THR
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 25 optimal weight:    0.0030
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:   20.0000
   chunk 36 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.093563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.070678 restraints weight = 19091.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.073652 restraints weight = 9988.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.075568 restraints weight = 6591.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.077114 restraints weight = 5083.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.078081 restraints weight = 4174.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.4966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6608  Z= 0.142
  Angle     :  0.678   9.484   8962  Z= 0.338
  Chirality :  0.041   0.143   1044
  Planarity :  0.004   0.036   1112
  Dihedral  :  4.910  17.892    896
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 22.13 %
    Favored  : 72.56 %
  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:  0.08 (0.29), residues: 812
  helix:  0.61 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.77 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 298 
 TYR   0.026   0.001   TYR B  75 
 PHE   0.035   0.002   PHE A 248 
 TRP   0.010   0.001   TRP B  44 
 HIS   0.015   0.002   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6608)
  covalent geometry    : angle       0.67826 ( 8962)
  hydrogen bonds       : bond        0.04346 (  466)
  hydrogen bonds       : angle       4.38284 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 113
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.9195 (t80)
REVERT: A  223 GLU cc_start: 0.8130 (tt0) cc_final: 0.7087 (tm-30)
REVERT: A  230 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7878 (t)
REVERT: A  279 ASP cc_start: 0.8876 (m-30) cc_final: 0.8561 (t70)
REVERT: A  280 GLU cc_start: 0.9432 (tp30) cc_final: 0.9173 (mt-10)
REVERT: A  303 GLN cc_start: 0.8293 (tp40) cc_final: 0.7877 (mm110)
REVERT: A  375 HIS cc_start: 0.9494 (m90) cc_final: 0.9021 (m90)
REVERT: A  459 GLN cc_start: 0.8837 (mt0) cc_final: 0.8439 (pt0)
REVERT: A  470 PHE cc_start: 0.8228 (m-80) cc_final: 0.7590 (m-80)
REVERT: B   45 GLN cc_start: 0.9330 (mm110) cc_final: 0.9056 (mp10)
REVERT: B  122 LEU cc_start: 0.9047 (mp) cc_final: 0.8836 (mm)
REVERT: B  230 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7849 (t)
REVERT: B  247 TYR cc_start: 0.8991 (t80) cc_final: 0.7753 (t80)
REVERT: B  248 PHE cc_start: 0.7776 (m-10) cc_final: 0.7122 (m-10)
REVERT: B  258 MET cc_start: 0.7953 (ptt) cc_final: 0.7565 (tmm)
REVERT: B  279 ASP cc_start: 0.8819 (m-30) cc_final: 0.8587 (t70)
REVERT: B  280 GLU cc_start: 0.9384 (tp30) cc_final: 0.9150 (mt-10)
REVERT: B  303 GLN cc_start: 0.8237 (tp40) cc_final: 0.7805 (mm110)
REVERT: B  375 HIS cc_start: 0.9469 (m90) cc_final: 0.9002 (m90)
REVERT: B  470 PHE cc_start: 0.8030 (m-80) cc_final: 0.7653 (m-80)
  outliers start: 37
  outliers final: 25
  residues processed: 140
  average time/residue: 0.0492
  time to fit residues: 10.0957
Evaluate side-chains
  121 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  262 GLU
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0980
   chunk 29 optimal weight:    0.1980
   chunk 0 optimal weight:   20.0000
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS
A 219 ASN
B 359 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.093207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.070117 restraints weight = 19152.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.073062 restraints weight = 10063.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.075061 restraints weight = 6689.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.076541 restraints weight = 5189.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.077363 restraints weight = 4260.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.5298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6608  Z= 0.137
  Angle     :  0.665  10.140   8962  Z= 0.330
  Chirality :  0.042   0.351   1044
  Planarity :  0.004   0.035   1112
  Dihedral  :  4.742  18.232    896
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 25.00 %
    Favored  : 70.69 %
  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:  0.32 (0.30), residues: 812
  helix:  0.80 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -1.82 (0.51), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 298 
 TYR   0.026   0.001   TYR B  75 
 PHE   0.034   0.002   PHE A 248 
 TRP   0.009   0.001   TRP B  44 
 HIS   0.013   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6608)
  covalent geometry    : angle       0.66530 ( 8962)
  hydrogen bonds       : bond        0.04155 (  466)
  hydrogen bonds       : angle       4.24169 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9167 (m)
REVERT: A  125 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.9172 (t80)
REVERT: A  223 GLU cc_start: 0.8074 (tt0) cc_final: 0.7087 (tm-30)
REVERT: A  230 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7706 (t)
REVERT: A  279 ASP cc_start: 0.8832 (m-30) cc_final: 0.8334 (t70)
REVERT: A  280 GLU cc_start: 0.9456 (tp30) cc_final: 0.9150 (mt-10)
REVERT: A  303 GLN cc_start: 0.8255 (tp40) cc_final: 0.7546 (mm110)
REVERT: A  375 HIS cc_start: 0.9479 (m90) cc_final: 0.9003 (m90)
REVERT: A  470 PHE cc_start: 0.8088 (m-80) cc_final: 0.7471 (m-80)
REVERT: A  496 GLU cc_start: 0.9238 (tp30) cc_final: 0.8467 (tp30)
REVERT: B  102 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8362 (t)
REVERT: B  106 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9029 (m)
REVERT: B  230 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7812 (t)
REVERT: B  247 TYR cc_start: 0.9072 (t80) cc_final: 0.7800 (t80)
REVERT: B  248 PHE cc_start: 0.8068 (m-80) cc_final: 0.7341 (m-10)
REVERT: B  279 ASP cc_start: 0.8818 (m-30) cc_final: 0.8352 (t0)
REVERT: B  280 GLU cc_start: 0.9345 (tp30) cc_final: 0.9129 (mt-10)
REVERT: B  303 GLN cc_start: 0.8290 (tp40) cc_final: 0.7888 (mm-40)
REVERT: B  375 HIS cc_start: 0.9470 (m90) cc_final: 0.8993 (m90)
REVERT: B  470 PHE cc_start: 0.8201 (m-80) cc_final: 0.7694 (m-80)
REVERT: B  496 GLU cc_start: 0.9261 (tp30) cc_final: 0.8671 (tp30)
  outliers start: 30
  outliers final: 19
  residues processed: 125
  average time/residue: 0.0581
  time to fit residues: 10.6326
Evaluate side-chains
  117 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
B 330 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.091680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.068664 restraints weight = 19398.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.071582 restraints weight = 10353.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.073375 restraints weight = 6926.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.074898 restraints weight = 5430.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.075604 restraints weight = 4473.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.5512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6608  Z= 0.169
  Angle     :  0.666   6.913   8962  Z= 0.340
  Chirality :  0.041   0.148   1044
  Planarity :  0.004   0.033   1112
  Dihedral  :  4.605  19.043    896
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 25.86 %
    Favored  : 69.54 %
  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:  0.53 (0.30), residues: 812
  helix:  0.93 (0.20), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.72 (0.51), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 294 
 TYR   0.025   0.002   TYR B  75 
 PHE   0.039   0.002   PHE A 248 
 TRP   0.011   0.002   TRP B  44 
 HIS   0.012   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6608)
  covalent geometry    : angle       0.66649 ( 8962)
  hydrogen bonds       : bond        0.04160 (  466)
  hydrogen bonds       : angle       4.25898 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.9183 (t80)
REVERT: A  223 GLU cc_start: 0.8113 (tt0) cc_final: 0.6946 (tm-30)
REVERT: A  230 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7970 (t)
REVERT: A  279 ASP cc_start: 0.8855 (m-30) cc_final: 0.8415 (t70)
REVERT: A  280 GLU cc_start: 0.9472 (tp30) cc_final: 0.9134 (mt-10)
REVERT: A  303 GLN cc_start: 0.8398 (tp40) cc_final: 0.7806 (tp-100)
REVERT: A  375 HIS cc_start: 0.9500 (m90) cc_final: 0.8987 (m90)
REVERT: A  470 PHE cc_start: 0.7951 (m-80) cc_final: 0.7350 (m-80)
REVERT: A  496 GLU cc_start: 0.9249 (tp30) cc_final: 0.8777 (tp30)
REVERT: B  106 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9054 (m)
REVERT: B  230 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7944 (t)
REVERT: B  258 MET cc_start: 0.8264 (ptt) cc_final: 0.7887 (ptm)
REVERT: B  280 GLU cc_start: 0.9408 (tp30) cc_final: 0.9187 (mt-10)
REVERT: B  303 GLN cc_start: 0.8436 (tp40) cc_final: 0.8066 (mm-40)
REVERT: B  375 HIS cc_start: 0.9482 (m90) cc_final: 0.9015 (m90)
REVERT: B  470 PHE cc_start: 0.8082 (m-80) cc_final: 0.7579 (m-80)
REVERT: B  496 GLU cc_start: 0.9267 (tp30) cc_final: 0.8715 (tp30)
  outliers start: 32
  outliers final: 24
  residues processed: 118
  average time/residue: 0.0529
  time to fit residues: 9.1856
Evaluate side-chains
  116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0870
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0970
   chunk 47 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.5556

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.093529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.070341 restraints weight = 18961.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.073273 restraints weight = 10270.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.075077 restraints weight = 6918.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.076636 restraints weight = 5452.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.077329 restraints weight = 4519.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.5818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6608  Z= 0.132
  Angle     :  0.648  10.157   8962  Z= 0.331
  Chirality :  0.041   0.189   1044
  Planarity :  0.004   0.034   1112
  Dihedral  :  4.582  19.764    896
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 27.16 %
    Favored  : 69.11 %
  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:  0.58 (0.30), residues: 812
  helix:  0.99 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.92 (0.51), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 294 
 TYR   0.027   0.001   TYR B  75 
 PHE   0.025   0.002   PHE B 148 
 TRP   0.016   0.001   TRP B  44 
 HIS   0.010   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6608)
  covalent geometry    : angle       0.64791 ( 8962)
  hydrogen bonds       : bond        0.04038 (  466)
  hydrogen bonds       : angle       4.21417 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.8064 (tt0) cc_final: 0.7011 (tm-30)
REVERT: A  230 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7746 (t)
REVERT: A  279 ASP cc_start: 0.8842 (m-30) cc_final: 0.8418 (t70)
REVERT: A  280 GLU cc_start: 0.9430 (tp30) cc_final: 0.9140 (mt-10)
REVERT: A  303 GLN cc_start: 0.8242 (tp40) cc_final: 0.7633 (tp-100)
REVERT: A  375 HIS cc_start: 0.9484 (m90) cc_final: 0.9010 (m90)
REVERT: A  470 PHE cc_start: 0.7896 (m-80) cc_final: 0.7544 (m-80)
REVERT: A  496 GLU cc_start: 0.9226 (tp30) cc_final: 0.8668 (tp30)
REVERT: B  102 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8389 (t)
REVERT: B  106 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9047 (m)
REVERT: B  230 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7769 (t)
REVERT: B  303 GLN cc_start: 0.8382 (tp40) cc_final: 0.7935 (mm-40)
REVERT: B  375 HIS cc_start: 0.9449 (m90) cc_final: 0.8976 (m90)
REVERT: B  470 PHE cc_start: 0.8013 (m-80) cc_final: 0.7734 (m-80)
REVERT: B  496 GLU cc_start: 0.9235 (tp30) cc_final: 0.8651 (tp30)
  outliers start: 26
  outliers final: 19
  residues processed: 110
  average time/residue: 0.0487
  time to fit residues: 8.1368
Evaluate side-chains
  104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 41 optimal weight:   20.0000
   chunk 5 optimal weight:    0.1980
   chunk 66 optimal weight:    0.0470
   chunk 34 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.5680

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.093465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.071121 restraints weight = 19362.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.074091 restraints weight = 10422.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.075848 restraints weight = 6991.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.077323 restraints weight = 5498.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.078092 restraints weight = 4551.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.6062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6608  Z= 0.127
  Angle     :  0.659   8.871   8962  Z= 0.330
  Chirality :  0.040   0.175   1044
  Planarity :  0.004   0.034   1112
  Dihedral  :  4.479  21.050    896
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 27.44 %
    Favored  : 68.82 %
  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:  0.84 (0.30), residues: 812
  helix:  1.19 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.93 (0.51), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 345 
 TYR   0.028   0.001   TYR B  75 
 PHE   0.025   0.002   PHE A 248 
 TRP   0.009   0.001   TRP B  44 
 HIS   0.012   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6608)
  covalent geometry    : angle       0.65854 ( 8962)
  hydrogen bonds       : bond        0.03907 (  466)
  hydrogen bonds       : angle       4.16597 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8470 (t)
REVERT: A  223 GLU cc_start: 0.8014 (tt0) cc_final: 0.6975 (tm-30)
REVERT: A  230 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7774 (t)
REVERT: A  279 ASP cc_start: 0.8834 (m-30) cc_final: 0.8534 (t70)
REVERT: A  303 GLN cc_start: 0.8210 (tp40) cc_final: 0.7413 (tt0)
REVERT: A  375 HIS cc_start: 0.9466 (m90) cc_final: 0.8973 (m90)
REVERT: A  470 PHE cc_start: 0.7916 (m-80) cc_final: 0.7589 (m-80)
REVERT: A  496 GLU cc_start: 0.9255 (tp30) cc_final: 0.8736 (tp30)
REVERT: B  102 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8474 (t)
REVERT: B  106 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9044 (m)
REVERT: B  230 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7827 (t)
REVERT: B  279 ASP cc_start: 0.9000 (t70) cc_final: 0.8738 (t70)
REVERT: B  303 GLN cc_start: 0.8356 (tp40) cc_final: 0.7924 (mm-40)
REVERT: B  375 HIS cc_start: 0.9434 (m90) cc_final: 0.8958 (m90)
REVERT: B  470 PHE cc_start: 0.7989 (m-80) cc_final: 0.7761 (m-80)
REVERT: B  496 GLU cc_start: 0.9256 (tp30) cc_final: 0.8647 (tp30)
  outliers start: 26
  outliers final: 19
  residues processed: 106
  average time/residue: 0.0539
  time to fit residues: 8.6414
Evaluate side-chains
  107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 53 optimal weight:    0.0980
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 15 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 384 ASN
** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.093922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.070576 restraints weight = 19618.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.073634 restraints weight = 10815.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.075526 restraints weight = 7321.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.077005 restraints weight = 5786.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.078007 restraints weight = 4827.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.6265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6608  Z= 0.128
  Angle     :  0.640   7.794   8962  Z= 0.327
  Chirality :  0.040   0.200   1044
  Planarity :  0.004   0.035   1112
  Dihedral  :  4.407  20.890    896
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 26.72 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.30), residues: 812
  helix:  1.30 (0.20), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.89 (0.51), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 294 
 TYR   0.028   0.001   TYR B  75 
 PHE   0.021   0.002   PHE B 148 
 TRP   0.009   0.001   TRP B 301 
 HIS   0.009   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6608)
  covalent geometry    : angle       0.63952 ( 8962)
  hydrogen bonds       : bond        0.03886 (  466)
  hydrogen bonds       : angle       4.14824 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8470 (t)
REVERT: A  223 GLU cc_start: 0.8039 (tt0) cc_final: 0.7009 (tm-30)
REVERT: A  230 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7782 (t)
REVERT: A  258 MET cc_start: 0.8064 (tmm) cc_final: 0.7846 (tmm)
REVERT: A  303 GLN cc_start: 0.8201 (tp40) cc_final: 0.7791 (mm-40)
REVERT: A  375 HIS cc_start: 0.9459 (m90) cc_final: 0.8972 (m90)
REVERT: A  470 PHE cc_start: 0.7842 (m-80) cc_final: 0.7509 (m-80)
REVERT: A  496 GLU cc_start: 0.9232 (tp30) cc_final: 0.8630 (tp30)
REVERT: B  102 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8437 (t)
REVERT: B  106 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.9044 (m)
REVERT: B  230 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7819 (t)
REVERT: B  303 GLN cc_start: 0.8268 (tp40) cc_final: 0.7908 (mm-40)
REVERT: B  375 HIS cc_start: 0.9428 (m90) cc_final: 0.8954 (m90)
REVERT: B  470 PHE cc_start: 0.7941 (m-80) cc_final: 0.7594 (m-80)
REVERT: B  496 GLU cc_start: 0.9245 (tp30) cc_final: 0.8594 (tp30)
  outliers start: 28
  outliers final: 21
  residues processed: 102
  average time/residue: 0.0507
  time to fit residues: 7.9072
Evaluate side-chains
  108 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  262 GLU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  299 PHE
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0060
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
B 390 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.093585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.071289 restraints weight = 19331.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.074273 restraints weight = 10584.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.076154 restraints weight = 7137.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.077636 restraints weight = 5554.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.078562 restraints weight = 4607.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.6430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6608  Z= 0.127
  Angle     :  0.639   7.619   8962  Z= 0.325
  Chirality :  0.040   0.212   1044
  Planarity :  0.004   0.035   1112
  Dihedral  :  4.340  18.709    896
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 27.44 %
    Favored  : 69.11 %
  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:  1.10 (0.30), residues: 812
  helix:  1.38 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.87 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 294 
 TYR   0.028   0.001   TYR B  75 
 PHE   0.025   0.002   PHE B 148 
 TRP   0.010   0.001   TRP B 301 
 HIS   0.008   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6608)
  covalent geometry    : angle       0.63923 ( 8962)
  hydrogen bonds       : bond        0.03857 (  466)
  hydrogen bonds       : angle       4.15307 ( 1386)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8411 (t)
REVERT: A  106 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9141 (m)
REVERT: A  223 GLU cc_start: 0.7939 (tt0) cc_final: 0.6945 (tm-30)
REVERT: A  258 MET cc_start: 0.8191 (tmm) cc_final: 0.7951 (tmm)
REVERT: A  303 GLN cc_start: 0.8227 (tp40) cc_final: 0.7812 (mm-40)
REVERT: A  375 HIS cc_start: 0.9455 (m90) cc_final: 0.8960 (m90)
REVERT: A  470 PHE cc_start: 0.7838 (m-80) cc_final: 0.7521 (m-80)
REVERT: A  496 GLU cc_start: 0.9233 (tp30) cc_final: 0.8629 (tp30)
REVERT: B  102 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (t)
REVERT: B  106 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9050 (m)
REVERT: B  303 GLN cc_start: 0.8318 (tp40) cc_final: 0.7924 (mm-40)
REVERT: B  375 HIS cc_start: 0.9420 (m90) cc_final: 0.8948 (m90)
REVERT: B  470 PHE cc_start: 0.8007 (m-80) cc_final: 0.7701 (m-80)
REVERT: B  496 GLU cc_start: 0.9238 (tp30) cc_final: 0.8619 (tp30)
  outliers start: 24
  outliers final: 18
  residues processed: 100
  average time/residue: 0.0525
  time to fit residues: 8.0772
Evaluate side-chains
  102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  324 CYS
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0770
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.7340

-------------------------------------------------------------------------------
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 = 0.3698 r_free = 0.3698 target = 0.094368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.070838 restraints weight = 19502.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.073873 restraints weight = 10860.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.075881 restraints weight = 7403.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.077281 restraints weight = 5783.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.078269 restraints weight = 4868.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.6561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6608  Z= 0.127
  Angle     :  0.646   8.725   8962  Z= 0.327
  Chirality :  0.040   0.224   1044
  Planarity :  0.004   0.036   1112
  Dihedral  :  4.304  17.271    896
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 27.73 %
    Favored  : 68.39 %
  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:  1.12 (0.30), residues: 812
  helix:  1.41 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.90 (0.50), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 294 
 TYR   0.027   0.001   TYR B  75 
 PHE   0.025   0.002   PHE B 248 
 TRP   0.011   0.001   TRP B  44 
 HIS   0.007   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6608)
  covalent geometry    : angle       0.64556 ( 8962)
  hydrogen bonds       : bond        0.03853 (  466)
  hydrogen bonds       : angle       4.14036 ( 1386)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1119.13 seconds
wall clock time: 20 minutes 5.57 seconds (1205.57 seconds total)