Starting phenix.real_space_refine
on Mon Apr  6 02:19:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wu4_21905/04_2026/6wu4_21905_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wu4_21905/04_2026/6wu4_21905.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wu4_21905/04_2026/6wu4_21905_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wu4_21905/04_2026/6wu4_21905_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wu4_21905/04_2026/6wu4_21905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wu4_21905/04_2026/6wu4_21905.map"
  }
  resolution = 3.71
  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=   0.000 sd=   0.266
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5034      2.51       5
     N    1176      2.21       5
     O    1260      1.98       5
     H    7812      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15332
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 489, 7666
          Classifications: {'peptide': 489}
          Link IDs: {'PTRANS': 22, 'TRANS': 466}
    Chain: "B"
      Number of atoms: 7666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 489, 7666
          Classifications: {'peptide': 489}
          Link IDs: {'PTRANS': 22, 'TRANS': 466}
  Time building chain proxies: 3.04, per 1000 atoms: 0.20
  Number of scatterers: 15332
  At special positions: 0
  Unit cell: (90.8725, 108.713, 76.935, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      50     16.00
     O    1260      8.00
     N    1176      7.00
     C    5034      6.00
     H    7812      1.00
    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: 1.55
  Conformation dependent library (CDL) restraints added in 569.1 milliseconds
  

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1784

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      81.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 11
    Processing helix  chain 'A' and resid 12 through 25
      removed outlier: 3.510A  pdb=" N   LEU A  16 " --> pdb=" O   PHE A  12 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA A  17 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 29
    Processing helix  chain 'A' and resid 35 through 54
    Processing helix  chain 'A' and resid 57 through 72
    Processing helix  chain 'A' and resid 91 through 95
    Processing helix  chain 'A' and resid 98 through 118
      removed outlier: 4.161A  pdb=" N   TRP A 102 " --> pdb=" O   ASN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 132
    Processing helix  chain 'A' and resid 135 through 150
      removed outlier: 4.042A  pdb=" N   GLY A 139 " --> pdb=" O   SER A 135 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   TYR A 140 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 160
      removed outlier: 3.649A  pdb=" N   THR A 160 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 175
      removed outlier: 3.578A  pdb=" N   VAL A 167 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 185
      removed outlier: 3.987A  pdb=" N   LYS A 185 " --> pdb=" O   PRO A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 206
    Processing helix  chain 'A' and resid 207 through 209
      No H-bonds generated for 'chain 'A' and resid 207 through 209'
    Processing helix  chain 'A' and resid 210 through 224
      removed outlier: 3.777A  pdb=" N   LEU A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 255
      removed outlier: 3.611A  pdb=" N   PHE A 233 " --> pdb=" O   TRP A 229 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   VAL A 238 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
      Proline residue:  A 248  - end of helix
    Processing helix  chain 'A' and resid 264 through 277
    Processing helix  chain 'A' and resid 280 through 300
    Processing helix  chain 'A' and resid 305 through 309
    Processing helix  chain 'A' and resid 311 through 325
    Processing helix  chain 'A' and resid 328 through 333
    Processing helix  chain 'A' and resid 335 through 359
      removed outlier: 3.998A  pdb=" N   TRP A 339 " --> pdb=" O   GLU A 335 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLY A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 372
      removed outlier: 3.657A  pdb=" N   VAL A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 392
    Processing helix  chain 'A' and resid 393 through 395
      No H-bonds generated for 'chain 'A' and resid 393 through 395'
    Processing helix  chain 'A' and resid 398 through 406
    Processing helix  chain 'A' and resid 406 through 415
    Processing helix  chain 'A' and resid 419 through 434
      removed outlier: 3.756A  pdb=" N   SER A 423 " --> pdb=" O   PRO A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 449
    Processing helix  chain 'A' and resid 455 through 485
    Processing helix  chain 'B' and resid 8 through 11
    Processing helix  chain 'B' and resid 12 through 25
      removed outlier: 3.511A  pdb=" N   LEU B  16 " --> pdb=" O   PHE B  12 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA B  17 " --> pdb=" O   ILE B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 29
    Processing helix  chain 'B' and resid 35 through 54
    Processing helix  chain 'B' and resid 57 through 72
    Processing helix  chain 'B' and resid 91 through 95
    Processing helix  chain 'B' and resid 98 through 118
      removed outlier: 4.160A  pdb=" N   TRP B 102 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 132
    Processing helix  chain 'B' and resid 135 through 150
      removed outlier: 4.040A  pdb=" N   GLY B 139 " --> pdb=" O   SER B 135 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR B 140 " --> pdb=" O   ILE B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 160
      removed outlier: 3.648A  pdb=" N   THR B 160 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 175
      removed outlier: 3.577A  pdb=" N   VAL B 167 " --> pdb=" O   VAL B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 185
      removed outlier: 3.985A  pdb=" N   LYS B 185 " --> pdb=" O   PRO B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 206
    Processing helix  chain 'B' and resid 207 through 209
      No H-bonds generated for 'chain 'B' and resid 207 through 209'
    Processing helix  chain 'B' and resid 210 through 224
      removed outlier: 3.778A  pdb=" N   LEU B 214 " --> pdb=" O   ALA B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 255
      removed outlier: 3.612A  pdb=" N   PHE B 233 " --> pdb=" O   TRP B 229 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   VAL B 238 " --> pdb=" O   TRP B 234 " (cutoff:3.500A)
      Proline residue:  B 239  - end of helix
      Proline residue:  B 248  - end of helix
    Processing helix  chain 'B' and resid 264 through 277
    Processing helix  chain 'B' and resid 280 through 300
    Processing helix  chain 'B' and resid 305 through 309
    Processing helix  chain 'B' and resid 311 through 325
    Processing helix  chain 'B' and resid 328 through 333
    Processing helix  chain 'B' and resid 335 through 359
      removed outlier: 3.998A  pdb=" N   TRP B 339 " --> pdb=" O   GLU B 335 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLY B 359 " --> pdb=" O   LEU B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 372
      removed outlier: 3.658A  pdb=" N   VAL B 372 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 392
    Processing helix  chain 'B' and resid 393 through 395
      No H-bonds generated for 'chain 'B' and resid 393 through 395'
    Processing helix  chain 'B' and resid 398 through 406
    Processing helix  chain 'B' and resid 406 through 415
    Processing helix  chain 'B' and resid 419 through 434
      removed outlier: 3.757A  pdb=" N   SER B 423 " --> pdb=" O   PRO B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 449
    Processing helix  chain 'B' and resid 455 through 485

    530 hydrogen bonds defined for protein.
    1548 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: 3.80

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 7808
        1.03 -     1.22: 4
        1.22 -     1.42: 3146
        1.42 -     1.61: 4492
        1.61 -     1.81: 96
  Bond restraints: 15546
  Sorted by residual:
  bond pdb=" C   ALA A  75 "
       pdb=" N   PRO A  76 "
    ideal  model  delta    sigma   weight residual
    1.331  1.310  0.021 1.21e-02 6.83e+03 3.09e+00
  bond pdb=" C   ALA B  75 "
       pdb=" N   PRO B  76 "
    ideal  model  delta    sigma   weight residual
    1.331  1.310  0.021 1.21e-02 6.83e+03 3.09e+00
  bond pdb=" CB  THR A 143 "
       pdb=" CG2 THR A 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.83e+00
  bond pdb=" CB  THR B 143 "
       pdb=" CG2 THR B 143 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.68e+00
  bond pdb=" CG1 ILE A 343 "
       pdb=" CD1 ILE A 343 "
    ideal  model  delta    sigma   weight residual
    1.513  1.453  0.060 3.90e-02 6.57e+02 2.34e+00
  ... (remaining 15541 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 26897
        1.33 -     2.66: 1286
        2.66 -     3.99: 73
        3.99 -     5.32: 24
        5.32 -     6.65: 2
  Bond angle restraints: 28282
  Sorted by residual:
  angle pdb=" N   GLY A  32 "
        pdb=" CA  GLY A  32 "
        pdb=" C   GLY A  32 "
      ideal   model   delta    sigma   weight residual
     114.61  110.37    4.24 1.49e+00 4.50e-01 8.08e+00
  angle pdb=" N   GLY B  32 "
        pdb=" CA  GLY B  32 "
        pdb=" C   GLY B  32 "
      ideal   model   delta    sigma   weight residual
     114.61  110.39    4.22 1.49e+00 4.50e-01 8.02e+00
  angle pdb=" C   ILE A 142 "
        pdb=" N   THR A 143 "
        pdb=" CA  THR A 143 "
      ideal   model   delta    sigma   weight residual
     120.28  117.04    3.24 1.34e+00 5.57e-01 5.83e+00
  angle pdb=" C   ILE B 142 "
        pdb=" N   THR B 143 "
        pdb=" CA  THR B 143 "
      ideal   model   delta    sigma   weight residual
     120.28  117.05    3.23 1.34e+00 5.57e-01 5.82e+00
  angle pdb=" CA  TRP A 344 "
        pdb=" CB  TRP A 344 "
        pdb=" CG  TRP A 344 "
      ideal   model   delta    sigma   weight residual
     113.60  117.49   -3.89 1.90e+00 2.77e-01 4.18e+00
  ... (remaining 28277 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 6334
       17.53 -    35.06: 662
       35.06 -    52.59: 205
       52.59 -    70.12: 60
       70.12 -    87.65: 13
  Dihedral angle restraints: 7274
    sinusoidal: 3848
      harmonic: 3426
  Sorted by residual:
  dihedral pdb=" CA  PRO B  57 "
           pdb=" C   PRO B  57 "
           pdb=" N   ILE B  58 "
           pdb=" CA  ILE B  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.07  -22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  PRO A  57 "
           pdb=" C   PRO A  57 "
           pdb=" N   ILE A  58 "
           pdb=" CA  ILE A  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.18  -22.82     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  LYS A  54 "
           pdb=" C   LYS A  54 "
           pdb=" N   PRO A  55 "
           pdb=" CA  PRO A  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.60   22.40     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 7271 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 612
       0.031 -    0.062: 375
       0.062 -    0.093: 211
       0.093 -    0.124: 38
       0.124 -    0.154: 6
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CA  ILE A 375 "
            pdb=" N   ILE A 375 "
            pdb=" C   ILE A 375 "
            pdb=" CB  ILE A 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.96e-01
  chirality pdb=" CA  ILE B 375 "
            pdb=" N   ILE B 375 "
            pdb=" C   ILE B 375 "
            pdb=" CB  ILE B 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.64e-01
  chirality pdb=" CA  PRO A  57 "
            pdb=" N   PRO A  57 "
            pdb=" C   PRO A  57 "
            pdb=" CB  PRO A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.82e-01
  ... (remaining 1239 not shown)

  Planarity restraints: 2186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 475 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.82e+00
        pdb=" C   GLY B 475 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   GLY B 475 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ILE B 476 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 475 "   -0.007 2.00e-02 2.50e+03   1.31e-02 1.73e+00
        pdb=" C   GLY A 475 "    0.023 2.00e-02 2.50e+03
        pdb=" O   GLY A 475 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ILE A 476 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 143 "    0.006 2.00e-02 2.50e+03   1.27e-02 1.62e+00
        pdb=" C   THR B 143 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   THR B 143 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLY B 144 "    0.007 2.00e-02 2.50e+03
  ... (remaining 2183 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 419
        2.11 -     2.74: 28614
        2.74 -     3.36: 44649
        3.36 -     3.98: 54541
        3.98 -     4.60: 88981
  Nonbonded interactions: 217204
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 475 "
            pdb=" HG1 THR A 479 "
     model   vdw
     1.493 2.450
  nonbonded pdb=" O   GLY B 475 "
            pdb=" HG1 THR B 479 "
     model   vdw
     1.553 2.450
  nonbonded pdb=" OE1 GLN A 307 "
            pdb=" H   GLN A 307 "
     model   vdw
     1.567 2.450
  nonbonded pdb=" OE1 GLN B 307 "
            pdb=" H   GLN B 307 "
     model   vdw
     1.569 2.450
  nonbonded pdb=" O   THR B 438 "
            pdb=" HE1 TRP B 459 "
     model   vdw
     1.587 2.450
  ... (remaining 217199 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: 0.02
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:             6.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.340
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
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      :  0.010   0.078   7734  Z= 0.402
  Angle     :  0.679   6.653  10550  Z= 0.372
  Chirality :  0.047   0.154   1242
  Planarity :  0.004   0.032   1254
  Dihedral  : 13.822  78.532   2650
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  : 12.73 %
    Favored  : 86.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  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: -4.78 (0.20), residues: 974
  helix: -2.48 (0.15), residues: 726
  sheet:  None (None), residues: 0
  loop : -4.82 (0.24), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 122 
 TYR   0.012   0.002   TYR B 255 
 PHE   0.015   0.002   PHE B 367 
 TRP   0.014   0.001   TRP A 344 
 HIS   0.005   0.002   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.01010 ( 7734)
  covalent geometry    : angle       0.67922 (10550)
  hydrogen bonds       : bond        0.13654 (  530)
  hydrogen bonds       : angle       6.63917 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ASN cc_start: 0.8662 (t0) cc_final: 0.8248 (t0)
REVERT: A  176 ASP cc_start: 0.8191 (t70) cc_final: 0.7442 (t0)
REVERT: A  286 MET cc_start: 0.7473 (tpt) cc_final: 0.7122 (tpt)
REVERT: A  335 GLU cc_start: 0.8229 (tp30) cc_final: 0.7701 (tp30)
REVERT: A  369 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8648 (tm-30)
REVERT: A  436 SER cc_start: 0.9276 (p) cc_final: 0.9035 (p)
REVERT: B    8 ASN cc_start: 0.8636 (t0) cc_final: 0.8261 (t0)
REVERT: B   10 LYS cc_start: 0.9138 (mtmt) cc_final: 0.8884 (mttm)
REVERT: B  176 ASP cc_start: 0.8229 (t70) cc_final: 0.7481 (t0)
REVERT: B  286 MET cc_start: 0.7481 (tpt) cc_final: 0.7138 (tpt)
REVERT: B  335 GLU cc_start: 0.8180 (tp30) cc_final: 0.7693 (tp30)
REVERT: B  369 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8659 (tm-30)
REVERT: B  436 SER cc_start: 0.9290 (p) cc_final: 0.9058 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1479
  time to fit residues: 31.9294
Evaluate side-chains
  128 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 264 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.119093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.097138 restraints weight = 31001.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.102299 restraints weight = 11122.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.105683 restraints weight = 5968.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.107951 restraints weight = 3991.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.109456 restraints weight = 3017.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7734  Z= 0.136
  Angle     :  0.583   5.192  10550  Z= 0.307
  Chirality :  0.040   0.160   1242
  Planarity :  0.004   0.037   1254
  Dihedral  :  4.568  20.834   1016
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.60 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 10.51 %
    Favored  : 89.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.25), residues: 974
  helix: -0.67 (0.18), residues: 750
  sheet:  None (None), residues: 0
  loop : -4.49 (0.27), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  29 
 TYR   0.009   0.001   TYR B 190 
 PHE   0.008   0.001   PHE B 193 
 TRP   0.013   0.001   TRP A 344 
 HIS   0.007   0.002   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7734)
  covalent geometry    : angle       0.58323 (10550)
  hydrogen bonds       : bond        0.04575 (  530)
  hydrogen bonds       : angle       5.02654 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 141
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 ASN cc_start: 0.8657 (t0) cc_final: 0.8229 (t0)
REVERT: A   10 LYS cc_start: 0.9234 (mtmt) cc_final: 0.8945 (mttm)
REVERT: A  176 ASP cc_start: 0.8253 (t70) cc_final: 0.7501 (t0)
REVERT: A  335 GLU cc_start: 0.8178 (tp30) cc_final: 0.7574 (tp30)
REVERT: A  369 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8792 (tm-30)
REVERT: B    8 ASN cc_start: 0.8656 (t0) cc_final: 0.8230 (t0)
REVERT: B   10 LYS cc_start: 0.9255 (mtmt) cc_final: 0.8963 (mttm)
REVERT: B  176 ASP cc_start: 0.8303 (t70) cc_final: 0.7549 (t0)
REVERT: B  286 MET cc_start: 0.7597 (tpt) cc_final: 0.7248 (tpt)
REVERT: B  335 GLU cc_start: 0.8135 (tp30) cc_final: 0.7560 (tp30)
REVERT: B  369 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8803 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 141
  average time/residue: 0.1359
  time to fit residues: 29.3502
Evaluate side-chains
  128 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain B residue   25 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.111867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.089773 restraints weight = 32296.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.094531 restraints weight = 12054.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.097787 restraints weight = 6715.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.099913 restraints weight = 4589.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.101283 restraints weight = 3541.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7734  Z= 0.173
  Angle     :  0.584   5.427  10550  Z= 0.306
  Chirality :  0.041   0.162   1242
  Planarity :  0.004   0.039   1254
  Dihedral  :  4.438  21.948   1016
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.16 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.53 %
    Favored  : 86.33 %
  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: -0.95 (0.27), residues: 974
  helix:  0.36 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -4.07 (0.30), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 184 
 TYR   0.012   0.001   TYR B 255 
 PHE   0.010   0.001   PHE B 193 
 TRP   0.013   0.001   TRP B 102 
 HIS   0.008   0.002   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7734)
  covalent geometry    : angle       0.58407 (10550)
  hydrogen bonds       : bond        0.04263 (  530)
  hydrogen bonds       : angle       4.77948 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 164
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A    8 ASN cc_start: 0.8726 (t0) cc_final: 0.8225 (t0)
REVERT: A   10 LYS cc_start: 0.9322 (mtmt) cc_final: 0.8994 (mttm)
REVERT: A   98 ASN cc_start: 0.8467 (t0) cc_final: 0.8188 (m-40)
REVERT: A  106 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8498 (mmm)
REVERT: A  176 ASP cc_start: 0.8343 (t70) cc_final: 0.7674 (t0)
REVERT: A  335 GLU cc_start: 0.8441 (tp30) cc_final: 0.7608 (tp30)
REVERT: A  434 ASN cc_start: 0.8736 (m110) cc_final: 0.8508 (m110)
REVERT: B    8 ASN cc_start: 0.8747 (t0) cc_final: 0.8266 (t0)
REVERT: B   10 LYS cc_start: 0.9328 (mtmt) cc_final: 0.9015 (mttm)
REVERT: B   98 ASN cc_start: 0.8432 (t0) cc_final: 0.8154 (m-40)
REVERT: B  176 ASP cc_start: 0.8409 (t70) cc_final: 0.7775 (t0)
REVERT: B  303 PHE cc_start: 0.7962 (m-80) cc_final: 0.7548 (m-80)
REVERT: B  335 GLU cc_start: 0.8388 (tp30) cc_final: 0.7980 (tp30)
  outliers start: 9
  outliers final: 7
  residues processed: 164
  average time/residue: 0.1359
  time to fit residues: 34.1373
Evaluate side-chains
  160 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  471 MET
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  485 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.130139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.108717 restraints weight = 31523.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.114089 restraints weight = 11079.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.117629 restraints weight = 5919.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.119881 restraints weight = 3927.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.121410 restraints weight = 2955.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7734  Z= 0.118
  Angle     :  0.540   5.533  10550  Z= 0.278
  Chirality :  0.039   0.160   1242
  Planarity :  0.004   0.038   1254
  Dihedral  :  4.348  21.629   1016
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.13 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 14.81 %
    Favored  : 84.56 %
  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: -0.12 (0.27), residues: 974
  helix:  0.91 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -3.59 (0.34), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 184 
 TYR   0.010   0.001   TYR A 252 
 PHE   0.007   0.001   PHE B 196 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.005   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7734)
  covalent geometry    : angle       0.53964 (10550)
  hydrogen bonds       : bond        0.03768 (  530)
  hydrogen bonds       : angle       4.46762 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 158
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A    8 ASN cc_start: 0.8712 (t0) cc_final: 0.8210 (t0)
REVERT: A   10 LYS cc_start: 0.9338 (mtmt) cc_final: 0.9006 (mttm)
REVERT: A  106 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8351 (mmm)
REVERT: A  176 ASP cc_start: 0.8305 (t70) cc_final: 0.7661 (t0)
REVERT: A  335 GLU cc_start: 0.8333 (tp30) cc_final: 0.7468 (tp30)
REVERT: A  434 ASN cc_start: 0.8596 (m110) cc_final: 0.8231 (m110)
REVERT: B    8 ASN cc_start: 0.8726 (t0) cc_final: 0.8248 (t0)
REVERT: B   10 LYS cc_start: 0.9335 (mtmt) cc_final: 0.9020 (mttm)
REVERT: B  174 SER cc_start: 0.9038 (t) cc_final: 0.8641 (p)
REVERT: B  176 ASP cc_start: 0.8398 (t70) cc_final: 0.7805 (t0)
REVERT: B  335 GLU cc_start: 0.8303 (tp30) cc_final: 0.7441 (tp30)
REVERT: B  434 ASN cc_start: 0.8623 (m110) cc_final: 0.8384 (m110)
  outliers start: 5
  outliers final: 2
  residues processed: 159
  average time/residue: 0.1363
  time to fit residues: 33.1060
Evaluate side-chains
  159 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain B residue  305 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.110397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.088221 restraints weight = 32403.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.092945 restraints weight = 12187.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.096147 restraints weight = 6814.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.098240 restraints weight = 4678.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.099606 restraints weight = 3634.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7734  Z= 0.144
  Angle     :  0.551   5.417  10550  Z= 0.286
  Chirality :  0.039   0.159   1242
  Planarity :  0.004   0.036   1254
  Dihedral  :  4.339  22.352   1016
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.75 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 15.32 %
    Favored  : 83.29 %
  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:  0.23 (0.28), residues: 974
  helix:  1.15 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -3.42 (0.35), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 159 
 TYR   0.025   0.001   TYR B 470 
 PHE   0.006   0.001   PHE B  96 
 TRP   0.012   0.001   TRP A 344 
 HIS   0.005   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 7734)
  covalent geometry    : angle       0.55080 (10550)
  hydrogen bonds       : bond        0.03823 (  530)
  hydrogen bonds       : angle       4.50795 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 171
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.9365 (mtmt) cc_final: 0.8967 (mttm)
REVERT: A   98 ASN cc_start: 0.8508 (t0) cc_final: 0.8218 (m-40)
REVERT: A  106 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8392 (mmm)
REVERT: A  176 ASP cc_start: 0.8378 (t70) cc_final: 0.7778 (t0)
REVERT: A  283 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8615 (mm-30)
REVERT: A  303 PHE cc_start: 0.7988 (m-80) cc_final: 0.7642 (m-10)
REVERT: A  335 GLU cc_start: 0.8401 (tp30) cc_final: 0.7844 (tp30)
REVERT: A  434 ASN cc_start: 0.8603 (m110) cc_final: 0.8201 (m110)
REVERT: B    8 ASN cc_start: 0.8782 (t0) cc_final: 0.8283 (t0)
REVERT: B   10 LYS cc_start: 0.9354 (mtmt) cc_final: 0.9035 (mttm)
REVERT: B   98 ASN cc_start: 0.8469 (t0) cc_final: 0.8212 (m-40)
REVERT: B  174 SER cc_start: 0.9084 (t) cc_final: 0.8676 (p)
REVERT: B  176 ASP cc_start: 0.8452 (t70) cc_final: 0.7879 (t0)
REVERT: B  303 PHE cc_start: 0.8038 (m-80) cc_final: 0.7594 (m-10)
REVERT: B  335 GLU cc_start: 0.8378 (tp30) cc_final: 0.7839 (tp30)
REVERT: B  434 ASN cc_start: 0.8650 (m110) cc_final: 0.8338 (m110)
REVERT: B  470 TYR cc_start: 0.7987 (m-80) cc_final: 0.7783 (m-80)
  outliers start: 11
  outliers final: 7
  residues processed: 173
  average time/residue: 0.1343
  time to fit residues: 35.5463
Evaluate side-chains
  173 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 165
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  471 MET
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  485 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.109624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.087434 restraints weight = 32720.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.092067 restraints weight = 12288.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.095286 restraints weight = 6884.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.097399 restraints weight = 4718.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.098815 restraints weight = 3654.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7734  Z= 0.140
  Angle     :  0.552   5.398  10550  Z= 0.287
  Chirality :  0.040   0.159   1242
  Planarity :  0.004   0.039   1254
  Dihedral  :  4.327  22.084   1016
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.03 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 17.34 %
    Favored  : 81.90 %
  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:  0.45 (0.28), residues: 974
  helix:  1.28 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop : -3.24 (0.36), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 134 
 TYR   0.015   0.001   TYR A 252 
 PHE   0.007   0.001   PHE A  96 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.005   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7734)
  covalent geometry    : angle       0.55213 (10550)
  hydrogen bonds       : bond        0.03763 (  530)
  hydrogen bonds       : angle       4.43536 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 176
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.9367 (mtmt) cc_final: 0.8968 (mttm)
REVERT: A  106 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8395 (mmm)
REVERT: A  174 SER cc_start: 0.9082 (t) cc_final: 0.8627 (p)
REVERT: A  176 ASP cc_start: 0.8356 (t70) cc_final: 0.7782 (t0)
REVERT: A  233 PHE cc_start: 0.8622 (t80) cc_final: 0.8290 (t80)
REVERT: A  283 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8583 (mm-30)
REVERT: A  303 PHE cc_start: 0.8033 (m-80) cc_final: 0.7678 (m-10)
REVERT: A  434 ASN cc_start: 0.8560 (m110) cc_final: 0.8147 (m110)
REVERT: B    8 ASN cc_start: 0.8797 (t0) cc_final: 0.8260 (t0)
REVERT: B   10 LYS cc_start: 0.9362 (mtmt) cc_final: 0.9025 (mttm)
REVERT: B  174 SER cc_start: 0.9035 (t) cc_final: 0.8558 (p)
REVERT: B  176 ASP cc_start: 0.8437 (t70) cc_final: 0.7898 (t0)
REVERT: B  303 PHE cc_start: 0.8097 (m-80) cc_final: 0.7652 (m-10)
REVERT: B  434 ASN cc_start: 0.8581 (m110) cc_final: 0.8250 (m110)
REVERT: B  470 TYR cc_start: 0.7914 (m-80) cc_final: 0.7714 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 177
  average time/residue: 0.1319
  time to fit residues: 35.7060
Evaluate side-chains
  180 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 175
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  471 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 92 optimal weight:    0.3980
   chunk 82 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.110128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.088302 restraints weight = 32214.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.092939 restraints weight = 12151.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.096053 restraints weight = 6790.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.098106 restraints weight = 4675.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.099407 restraints weight = 3640.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7734  Z= 0.117
  Angle     :  0.533   5.314  10550  Z= 0.275
  Chirality :  0.039   0.158   1242
  Planarity :  0.004   0.039   1254
  Dihedral  :  4.279  22.775   1016
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.65 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 17.72 %
    Favored  : 81.65 %
  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:  0.89 (0.28), residues: 974
  helix:  1.59 (0.19), residues: 742
  sheet:  None (None), residues: 0
  loop : -2.87 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 184 
 TYR   0.014   0.001   TYR B 470 
 PHE   0.005   0.001   PHE B 196 
 TRP   0.013   0.001   TRP A 344 
 HIS   0.005   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7734)
  covalent geometry    : angle       0.53341 (10550)
  hydrogen bonds       : bond        0.03570 (  530)
  hydrogen bonds       : angle       4.32133 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 180
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.9374 (mtmt) cc_final: 0.8964 (mttm)
REVERT: A  174 SER cc_start: 0.9064 (t) cc_final: 0.8574 (p)
REVERT: A  176 ASP cc_start: 0.8355 (t70) cc_final: 0.7782 (t0)
REVERT: A  233 PHE cc_start: 0.8519 (t80) cc_final: 0.8183 (t80)
REVERT: A  303 PHE cc_start: 0.8010 (m-80) cc_final: 0.7636 (m-10)
REVERT: A  416 MET cc_start: 0.8597 (mmm) cc_final: 0.8308 (mmt)
REVERT: A  434 ASN cc_start: 0.8443 (m110) cc_final: 0.7995 (m110)
REVERT: B    8 ASN cc_start: 0.8736 (t0) cc_final: 0.8177 (t0)
REVERT: B   10 LYS cc_start: 0.9365 (mtmt) cc_final: 0.9021 (mttm)
REVERT: B  174 SER cc_start: 0.9015 (t) cc_final: 0.8587 (p)
REVERT: B  176 ASP cc_start: 0.8405 (t70) cc_final: 0.7877 (t0)
REVERT: B  303 PHE cc_start: 0.8054 (m-80) cc_final: 0.7597 (m-10)
REVERT: B  434 ASN cc_start: 0.8482 (m110) cc_final: 0.8113 (m110)
  outliers start: 5
  outliers final: 4
  residues processed: 181
  average time/residue: 0.1335
  time to fit residues: 37.0985
Evaluate side-chains
  179 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 175
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  471 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.108525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.086480 restraints weight = 32998.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.091120 restraints weight = 12157.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.094268 restraints weight = 6739.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.096321 restraints weight = 4632.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.097637 restraints weight = 3594.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7734  Z= 0.147
  Angle     :  0.552   5.220  10550  Z= 0.286
  Chirality :  0.039   0.159   1242
  Planarity :  0.004   0.039   1254
  Dihedral  :  4.302  22.207   1016
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.85 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 18.35 %
    Favored  : 81.01 %
  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:  0.97 (0.28), residues: 974
  helix:  1.63 (0.19), residues: 742
  sheet:  None (None), residues: 0
  loop : -2.76 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 134 
 TYR   0.015   0.001   TYR B 470 
 PHE   0.007   0.001   PHE A  96 
 TRP   0.013   0.001   TRP A 344 
 HIS   0.005   0.002   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7734)
  covalent geometry    : angle       0.55151 (10550)
  hydrogen bonds       : bond        0.03716 (  530)
  hydrogen bonds       : angle       4.36499 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 184
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.9377 (mtmt) cc_final: 0.8965 (mttm)
REVERT: A  174 SER cc_start: 0.9096 (t) cc_final: 0.8600 (p)
REVERT: A  176 ASP cc_start: 0.8389 (t70) cc_final: 0.7840 (t0)
REVERT: A  233 PHE cc_start: 0.8526 (t80) cc_final: 0.8176 (t80)
REVERT: A  303 PHE cc_start: 0.8046 (m-80) cc_final: 0.7673 (m-10)
REVERT: A  416 MET cc_start: 0.8594 (mmm) cc_final: 0.8304 (mmt)
REVERT: A  434 ASN cc_start: 0.8481 (m110) cc_final: 0.8041 (m110)
REVERT: B   10 LYS cc_start: 0.9364 (mtmt) cc_final: 0.8970 (mttm)
REVERT: B  176 ASP cc_start: 0.8417 (t70) cc_final: 0.7960 (t0)
REVERT: B  303 PHE cc_start: 0.8116 (m-80) cc_final: 0.7670 (m-10)
REVERT: B  434 ASN cc_start: 0.8456 (m110) cc_final: 0.8083 (m110)
  outliers start: 5
  outliers final: 4
  residues processed: 185
  average time/residue: 0.1451
  time to fit residues: 40.2393
Evaluate side-chains
  186 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 182
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  471 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.107860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.085492 restraints weight = 32642.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.090159 restraints weight = 12366.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.093299 restraints weight = 6951.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.095346 restraints weight = 4807.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.096650 restraints weight = 3759.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7734  Z= 0.142
  Angle     :  0.549   5.639  10550  Z= 0.284
  Chirality :  0.039   0.159   1242
  Planarity :  0.004   0.039   1254
  Dihedral  :  4.293  22.691   1016
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.85 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 18.48 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.28), residues: 974
  helix:  1.70 (0.19), residues: 742
  sheet:  None (None), residues: 0
  loop : -2.59 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 134 
 TYR   0.014   0.001   TYR A 252 
 PHE   0.006   0.001   PHE B  96 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.005   0.002   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7734)
  covalent geometry    : angle       0.54856 (10550)
  hydrogen bonds       : bond        0.03683 (  530)
  hydrogen bonds       : angle       4.33973 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 184
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.9386 (mtmt) cc_final: 0.8980 (mttm)
REVERT: A  176 ASP cc_start: 0.8413 (t70) cc_final: 0.7900 (t0)
REVERT: A  233 PHE cc_start: 0.8659 (t80) cc_final: 0.8280 (t80)
REVERT: A  303 PHE cc_start: 0.8122 (m-80) cc_final: 0.7776 (m-10)
REVERT: A  416 MET cc_start: 0.8546 (mmm) cc_final: 0.8234 (mmt)
REVERT: A  434 ASN cc_start: 0.8466 (m110) cc_final: 0.8029 (m110)
REVERT: B   10 LYS cc_start: 0.9374 (mtmt) cc_final: 0.8984 (mttm)
REVERT: B  176 ASP cc_start: 0.8381 (t70) cc_final: 0.7956 (t0)
REVERT: B  303 PHE cc_start: 0.8198 (m-80) cc_final: 0.7741 (m-10)
REVERT: B  434 ASN cc_start: 0.8468 (m110) cc_final: 0.8091 (m110)
  outliers start: 5
  outliers final: 5
  residues processed: 184
  average time/residue: 0.1286
  time to fit residues: 36.2644
Evaluate side-chains
  185 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 180
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  485 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.106983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.085556 restraints weight = 32327.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.090041 restraints weight = 12403.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.093001 restraints weight = 6948.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.095038 restraints weight = 4805.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.096212 restraints weight = 3736.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7734  Z= 0.155
  Angle     :  0.553   5.152  10550  Z= 0.289
  Chirality :  0.040   0.161   1242
  Planarity :  0.004   0.039   1254
  Dihedral  :  4.310  22.066   1016
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.85 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 18.73 %
    Favored  : 80.51 %
  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:  1.15 (0.28), residues: 974
  helix:  1.70 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -2.47 (0.39), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 134 
 TYR   0.016   0.001   TYR A 252 
 PHE   0.007   0.001   PHE B  96 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.005   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 7734)
  covalent geometry    : angle       0.55269 (10550)
  hydrogen bonds       : bond        0.03755 (  530)
  hydrogen bonds       : angle       4.37365 ( 1548)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 188
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.9380 (mtmt) cc_final: 0.8963 (mttm)
REVERT: A  176 ASP cc_start: 0.8390 (t70) cc_final: 0.7869 (t0)
REVERT: A  233 PHE cc_start: 0.8533 (t80) cc_final: 0.8100 (t80)
REVERT: A  303 PHE cc_start: 0.8133 (m-80) cc_final: 0.7750 (m-10)
REVERT: A  416 MET cc_start: 0.8628 (mmm) cc_final: 0.8289 (mmt)
REVERT: B   10 LYS cc_start: 0.9373 (mtmt) cc_final: 0.8974 (mttm)
REVERT: B  176 ASP cc_start: 0.8370 (t70) cc_final: 0.7958 (t0)
REVERT: B  303 PHE cc_start: 0.8189 (m-80) cc_final: 0.7735 (m-10)
REVERT: B  416 MET cc_start: 0.8605 (mmm) cc_final: 0.8311 (mmt)
REVERT: B  434 ASN cc_start: 0.8414 (m110) cc_final: 0.8024 (m110)
  outliers start: 6
  outliers final: 5
  residues processed: 188
  average time/residue: 0.1386
  time to fit residues: 39.8229
Evaluate side-chains
  191 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 186
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  471 MET
Chi-restraints excluded: chain B residue  485 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0570
   overall best weight:    0.8900

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

Flipped N/Q/H residues before XYZ refinement:
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.108116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.086719 restraints weight = 32086.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.091254 restraints weight = 12267.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.094273 restraints weight = 6869.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.096298 restraints weight = 4713.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.097678 restraints weight = 3661.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7734  Z= 0.127
  Angle     :  0.539   5.312  10550  Z= 0.279
  Chirality :  0.039   0.155   1242
  Planarity :  0.004   0.041   1254
  Dihedral  :  4.289  22.881   1016
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.44 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 19.37 %
    Favored  : 80.00 %
  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:  1.31 (0.28), residues: 974
  helix:  1.80 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -2.34 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 134 
 TYR   0.020   0.001   TYR A 252 
 PHE   0.028   0.001   PHE B 312 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.005   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7734)
  covalent geometry    : angle       0.53859 (10550)
  hydrogen bonds       : bond        0.03637 (  530)
  hydrogen bonds       : angle       4.30396 ( 1548)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2528.56 seconds
wall clock time: 43 minutes 50.61 seconds (2630.61 seconds total)