Starting phenix.real_space_refine
on Tue Feb  3 15:57:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f2m_28822/02_2026/8f2m_28822.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f2m_28822/02_2026/8f2m_28822.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f2m_28822/02_2026/8f2m_28822.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f2m_28822/02_2026/8f2m_28822.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f2m_28822/02_2026/8f2m_28822.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f2m_28822/02_2026/8f2m_28822.cif"
  }
  resolution = 3.7
  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=   0.001 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       9      5.16       5
     C    2970      2.51       5
     N     794      2.21       5
     O     923      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4696
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 3425
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 434, 3425
          Classifications: {'peptide': 434}
          Link IDs: {'PTRANS': 11, 'TRANS': 422}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 589
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 2, 'TRANS': 70}
    Chain: "B"
      Number of atoms: 589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 589
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 2, 'TRANS': 70}
    Chain: "C"
      Number of atoms: 93
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 93
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
  Time building chain proxies: 1.24, per 1000 atoms: 0.26
  Number of scatterers: 4696
  At special positions: 0
  Unit cell: (101.556, 108.108, 126.672, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       9     16.00
     O     923      8.00
     N     794      7.00
     C    2970      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 298.6 milliseconds
  

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1124

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 6 sheets defined
      45.6% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'D' and resid 14 through 18
      removed outlier: 3.748A  pdb=" N   TYR D  18 " --> pdb=" O   THR D  15 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 52
    Processing helix  chain 'D' and resid 54 through 78
      removed outlier: 3.625A  pdb=" N   ILE D  69 " --> pdb=" O   LEU D  65 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 85
      No H-bonds generated for 'chain 'D' and resid 83 through 85'
    Processing helix  chain 'D' and resid 111 through 118
      removed outlier: 3.743A  pdb=" N   GLN D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LYS D 118 " --> pdb=" O   GLU D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 146 through 152
    Processing helix  chain 'D' and resid 157 through 192
      removed outlier: 3.703A  pdb=" N   ASN D 172 " --> pdb=" O   ASN D 168 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   SER D 173 " --> pdb=" O   ALA D 169 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA D 174 " --> pdb=" O   ILE D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 225
      removed outlier: 3.548A  pdb=" N   THR D 225 " --> pdb=" O   ALA D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 245
      No H-bonds generated for 'chain 'D' and resid 243 through 245'
    Processing helix  chain 'D' and resid 253 through 259
      removed outlier: 3.673A  pdb=" N   GLU D 258 " --> pdb=" O   ASP D 254 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU D 259 " --> pdb=" O   LEU D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 268
      removed outlier: 4.554A  pdb=" N   LEU D 264 " --> pdb=" O   ASP D 260 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   LYS D 266 " --> pdb=" O   ASP D 262 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   PHE D 268 " --> pdb=" O   LEU D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 275
    Processing helix  chain 'F' and resid 4 through 15
      removed outlier: 3.601A  pdb=" N   ASP F  10 " --> pdb=" O   GLU F   6 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ILE F  11 " --> pdb=" O   GLU F   7 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 74
      removed outlier: 3.789A  pdb=" N   LEU F  32 " --> pdb=" O   ALA F  28 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU F  46 " --> pdb=" O   GLU F  42 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ALA F  55 " --> pdb=" O   GLU F  51 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   THR F  74 " --> pdb=" O   GLN F  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 17
      removed outlier: 3.649A  pdb=" N   ILE B  11 " --> pdb=" O   GLU B   7 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU B  12 " --> pdb=" O   HIS B   8 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASN B  13 " --> pdb=" O   GLU B   9 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP B  17 " --> pdb=" O   ASN B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 73
      removed outlier: 3.954A  pdb=" N   THR B  26 " --> pdb=" O   GLN B  22 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS B  52 " --> pdb=" O   LYS B  48 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA B  54 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 87 through 90
      removed outlier: 5.044A  pdb=" N   ASP D 304 " --> pdb=" O   LYS D  88 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   GLN D  90 " --> pdb=" O   ASP D 304 " (cutoff:3.500A)
      removed outlier: 9.992A  pdb=" N   LEU D 306 " --> pdb=" O   GLN D  90 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   TRP D 327 " --> pdb=" O   ASN D 305 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   HIS D 307 " --> pdb=" O   HIS D 325 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   HIS D 325 " --> pdb=" O   HIS D 307 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLY D 138 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 143 through 145
      removed outlier: 3.684A  pdb=" N   TYR D 319 " --> pdb=" O   ASN D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 279 through 282
    Processing sheet with id=AA4, first strand: chain 'D' and resid 349 through 354
      removed outlier: 4.419A  pdb=" N   GLN D 351 " --> pdb=" O   ARG D 374 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ARG D 374 " --> pdb=" O   GLN D 351 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 358 through 361
      removed outlier: 5.988A  pdb=" N   ALA D 359 " --> pdb=" O   SER D 436 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL D 429 " --> pdb=" O   VAL D 418 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 366 through 368
      removed outlier: 3.632A  pdb=" N   ALA D 395 " --> pdb=" O   SER D 403 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    654 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.70

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1563
        1.34 -     1.46: 693
        1.46 -     1.57: 2500
        1.57 -     1.69: 1
        1.69 -     1.81: 18
  Bond restraints: 4775
  Sorted by residual:
  bond pdb=" CB  PRO D 356 "
       pdb=" CG  PRO D 356 "
    ideal  model  delta    sigma   weight residual
    1.492  1.581 -0.089 5.00e-02 4.00e+02 3.13e+00
  bond pdb=" C   SER D 355 "
       pdb=" N   PRO D 356 "
    ideal  model  delta    sigma   weight residual
    1.334  1.366 -0.032 2.34e-02 1.83e+03 1.89e+00
  bond pdb=" CG  PRO B  18 "
       pdb=" CD  PRO B  18 "
    ideal  model  delta    sigma   weight residual
    1.503  1.544 -0.041 3.40e-02 8.65e+02 1.43e+00
  bond pdb=" CG  PRO D 356 "
       pdb=" CD  PRO D 356 "
    ideal  model  delta    sigma   weight residual
    1.503  1.544 -0.041 3.40e-02 8.65e+02 1.43e+00
  bond pdb=" CB  LYS D 215 "
       pdb=" CG  LYS D 215 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.26e+00
  ... (remaining 4770 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 6221
        1.49 -     2.98: 191
        2.98 -     4.48: 39
        4.48 -     5.97: 11
        5.97 -     7.46: 5
  Bond angle restraints: 6467
  Sorted by residual:
  angle pdb=" CA  PRO D 356 "
        pdb=" N   PRO D 356 "
        pdb=" CD  PRO D 356 "
      ideal   model   delta    sigma   weight residual
     112.00  106.76    5.24 1.40e+00 5.10e-01 1.40e+01
  angle pdb=" CA  LYS D 223 "
        pdb=" CB  LYS D 223 "
        pdb=" CG  LYS D 223 "
      ideal   model   delta    sigma   weight residual
     114.10  120.94   -6.84 2.00e+00 2.50e-01 1.17e+01
  angle pdb=" CB  LYS D 215 "
        pdb=" CG  LYS D 215 "
        pdb=" CD  LYS D 215 "
      ideal   model   delta    sigma   weight residual
     111.30  118.76   -7.46 2.30e+00 1.89e-01 1.05e+01
  angle pdb=" N   SER D  34 "
        pdb=" CA  SER D  34 "
        pdb=" C   SER D  34 "
      ideal   model   delta    sigma   weight residual
     114.39  109.85    4.54 1.45e+00 4.76e-01 9.81e+00
  angle pdb=" C   TYR D  18 "
        pdb=" N   ASP D  19 "
        pdb=" CA  ASP D  19 "
      ideal   model   delta    sigma   weight residual
     121.54  127.34   -5.80 1.91e+00 2.74e-01 9.21e+00
  ... (remaining 6462 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 2491
       17.70 -    35.41: 306
       35.41 -    53.11: 81
       53.11 -    70.81: 12
       70.81 -    88.52: 2
  Dihedral angle restraints: 2892
    sinusoidal: 1160
      harmonic: 1732
  Sorted by residual:
  dihedral pdb=" CA  TYR D  18 "
           pdb=" C   TYR D  18 "
           pdb=" N   ASP D  19 "
           pdb=" CA  ASP D  19 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.29   26.71     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  SER D 355 "
           pdb=" C   SER D 355 "
           pdb=" N   PRO D 356 "
           pdb=" CA  PRO D 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.43  -22.57     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  ILE D 170 "
           pdb=" C   ILE D 170 "
           pdb=" N   TYR D 171 "
           pdb=" CA  TYR D 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.67  -18.33     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 2889 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 534
       0.038 -    0.075: 154
       0.075 -    0.112: 46
       0.112 -    0.150: 10
       0.150 -    0.187: 2
  Chirality restraints: 746
  Sorted by residual:
  chirality pdb=" CA  PRO D 356 "
            pdb=" N   PRO D 356 "
            pdb=" C   PRO D 356 "
            pdb=" CB  PRO D 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.79e-01
  chirality pdb=" CA  PRO B  18 "
            pdb=" N   PRO B  18 "
            pdb=" C   PRO B  18 "
            pdb=" CB  PRO B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 6.92e-01
  chirality pdb=" CA  ASP D  19 "
            pdb=" N   ASP D  19 "
            pdb=" C   ASP D  19 "
            pdb=" CB  ASP D  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.53e-01
  ... (remaining 743 not shown)

  Planarity restraints: 834
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 355 "    0.082 5.00e-02 4.00e+02   1.24e-01 2.47e+01
        pdb=" N   PRO D 356 "   -0.215 5.00e-02 4.00e+02
        pdb=" CA  PRO D 356 "    0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO D 356 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 226 "   -0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO D 227 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO D 227 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 227 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B   4 "   -0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO B   5 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B   5 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B   5 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 831 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1022
        2.78 -     3.31: 4429
        3.31 -     3.84: 7211
        3.84 -     4.37: 8206
        4.37 -     4.90: 13799
  Nonbonded interactions: 34667
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D  87 "
            pdb=" OE2 GLU D 178 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OG  SER D  11 "
            pdb=" OG  SER D  17 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG  SER D 405 "
            pdb=" OE2 GLU D 408 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   GLY D 390 "
            pdb=" ND2 ASN D 410 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" OG1 THR D  15 "
            pdb=" OE2 GLU D 160 "
     model   vdw
     2.268 3.040
  ... (remaining 34662 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}

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:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.530
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
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      :  0.003   0.089   4775  Z= 0.147
  Angle     :  0.671   7.461   6467  Z= 0.380
  Chirality :  0.040   0.187    746
  Planarity :  0.006   0.124    834
  Dihedral  : 16.382  88.515   1768
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  4.98 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 24.18 %
    Favored  : 75.43 %
  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: -0.85 (0.34), residues: 582
  helix:  0.70 (0.32), residues: 256
  sheet: -0.62 (0.47), residues: 115
  loop : -2.10 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 239 
 TYR   0.019   0.002   TYR D 324 
 PHE   0.019   0.001   PHE D 162 
 TRP   0.018   0.002   TRP D 320 
 HIS   0.003   0.001   HIS D 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4775)
  covalent geometry    : angle       0.67136 ( 6467)
  hydrogen bonds       : bond        0.23061 (  224)
  hydrogen bonds       : angle       7.46775 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   25 ARG cc_start: 0.5800 (mtm180) cc_final: 0.4943 (mtp-110)
REVERT: F   46 LEU cc_start: 0.8103 (tp) cc_final: 0.7800 (mm)
REVERT: B   25 ARG cc_start: 0.6595 (ttt-90) cc_final: 0.5887 (tpt-90)
  outliers start: 2
  outliers final: 2
  residues processed: 88
  average time/residue: 0.0979
  time to fit residues: 10.5947
Evaluate side-chains
  72 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue  279 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:   30.0000
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:   30.0000
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0470
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
D  58 GLN
** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 248 HIS
D 368 GLN
F  22 GLN
F  64 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.178938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.154771 restraints weight = 7082.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.150796 restraints weight = 11352.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.145809 restraints weight = 9886.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.145721 restraints weight = 12729.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.145884 restraints weight = 9503.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   4775  Z= 0.140
  Angle     :  0.610   7.481   6467  Z= 0.332
  Chirality :  0.042   0.218    746
  Planarity :  0.006   0.125    834
  Dihedral  :  4.909  33.449    636
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  :  5.50 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.69 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.35), residues: 582
  helix:  1.23 (0.32), residues: 259
  sheet: -0.51 (0.46), residues: 126
  loop : -2.05 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  95 
 TYR   0.014   0.002   TYR F  36 
 PHE   0.031   0.002   PHE F  68 
 TRP   0.008   0.001   TRP D 299 
 HIS   0.004   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4775)
  covalent geometry    : angle       0.60991 ( 6467)
  hydrogen bonds       : bond        0.06302 (  224)
  hydrogen bonds       : angle       4.82329 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: D   80 ASN cc_start: 0.7319 (p0) cc_final: 0.6783 (p0)
REVERT: D  326 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9040 (p)
REVERT: F   22 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.5509 (tp-100)
REVERT: B   43 TYR cc_start: 0.6872 (t80) cc_final: 0.6516 (t80)
  outliers start: 13
  outliers final: 5
  residues processed: 90
  average time/residue: 0.0975
  time to fit residues: 10.9784
Evaluate side-chains
  69 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  326 VAL
Chi-restraints excluded: chain D residue  402 LEU
Chi-restraints excluded: chain F residue   22 GLN
Chi-restraints excluded: chain F residue   53 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    0.1980
   overall best weight:    3.4388

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

Flipped N/Q/H residues before XYZ refinement:
D  58 GLN
** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 337 ASN
F   8 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.168319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.135465 restraints weight = 7065.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.132451 restraints weight = 13323.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.134288 restraints weight = 12386.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.133969 restraints weight = 7829.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.134154 restraints weight = 8600.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   4775  Z= 0.188
  Angle     :  0.658   8.721   6467  Z= 0.358
  Chirality :  0.044   0.205    746
  Planarity :  0.006   0.127    834
  Dihedral  :  5.034  28.349    633
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  5.67 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.31 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.34), residues: 582
  helix:  1.34 (0.32), residues: 252
  sheet: -0.58 (0.46), residues: 126
  loop : -2.27 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 239 
 TYR   0.017   0.002   TYR D 324 
 PHE   0.030   0.002   PHE D 162 
 TRP   0.017   0.002   TRP D 299 
 HIS   0.005   0.001   HIS D 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 4775)
  covalent geometry    : angle       0.65760 ( 6467)
  hydrogen bonds       : bond        0.06662 (  224)
  hydrogen bonds       : angle       4.68300 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: D   74 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7832 (mt)
REVERT: D   80 ASN cc_start: 0.7684 (p0) cc_final: 0.7182 (p0)
REVERT: D  147 ASP cc_start: 0.7329 (m-30) cc_final: 0.7067 (m-30)
REVERT: D  256 GLU cc_start: 0.7253 (tp30) cc_final: 0.7045 (tp30)
REVERT: F   22 GLN cc_start: 0.6136 (pp30) cc_final: 0.5328 (tp-100)
REVERT: B   43 TYR cc_start: 0.7001 (t80) cc_final: 0.6529 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0760
  time to fit residues: 9.7317
Evaluate side-chains
  81 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   99 GLU
Chi-restraints excluded: chain D residue  170 ILE
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  402 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 8 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
D  55 GLN
** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 271 ASN
B  64 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.157844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.125368 restraints weight = 7149.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.121793 restraints weight = 13574.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.123459 restraints weight = 13726.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.123924 restraints weight = 7951.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.124493 restraints weight = 7045.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.4563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   4775  Z= 0.292
  Angle     :  0.746   8.888   6467  Z= 0.411
  Chirality :  0.048   0.194    746
  Planarity :  0.007   0.131    834
  Dihedral  :  5.732  35.172    633
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  6.53 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 20.54 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    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: -0.79 (0.34), residues: 582
  helix:  0.89 (0.31), residues: 266
  sheet: -0.65 (0.45), residues: 123
  loop : -2.45 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 239 
 TYR   0.019   0.003   TYR D 140 
 PHE   0.029   0.003   PHE D 162 
 TRP   0.020   0.002   TRP D 299 
 HIS   0.007   0.002   HIS D 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00695 ( 4775)
  covalent geometry    : angle       0.74643 ( 6467)
  hydrogen bonds       : bond        0.07631 (  224)
  hydrogen bonds       : angle       4.87542 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.233 
Fit side-chains
REVERT: D   80 ASN cc_start: 0.8117 (p0) cc_final: 0.7631 (p0)
REVERT: F   22 GLN cc_start: 0.5768 (pp30) cc_final: 0.5436 (tp-100)
REVERT: B   43 TYR cc_start: 0.7265 (t80) cc_final: 0.6592 (t80)
  outliers start: 24
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0681
  time to fit residues: 8.3140
Evaluate side-chains
  73 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   99 GLU
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  170 ILE
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  346 VAL
Chi-restraints excluded: chain D residue  402 LEU
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain B residue   16 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 35 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    2.0066

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

Flipped N/Q/H residues before XYZ refinement:
D 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.162428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.130107 restraints weight = 7169.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.129176 restraints weight = 15289.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.130640 restraints weight = 14136.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.130740 restraints weight = 8373.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.131146 restraints weight = 8746.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.4664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   4775  Z= 0.147
  Angle     :  0.628   9.529   6467  Z= 0.345
  Chirality :  0.043   0.222    746
  Planarity :  0.006   0.126    834
  Dihedral  :  5.067  33.209    633
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  5.84 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 23.03 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.35), residues: 582
  helix:  1.18 (0.32), residues: 259
  sheet: -0.35 (0.48), residues: 122
  loop : -2.44 (0.40), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 239 
 TYR   0.016   0.002   TYR D 140 
 PHE   0.017   0.001   PHE D 162 
 TRP   0.009   0.001   TRP D 299 
 HIS   0.004   0.001   HIS F   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4775)
  covalent geometry    : angle       0.62756 ( 6467)
  hydrogen bonds       : bond        0.06230 (  224)
  hydrogen bonds       : angle       4.55570 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.198 
Fit side-chains
REVERT: D   80 ASN cc_start: 0.7739 (p0) cc_final: 0.7495 (p0)
REVERT: B   43 TYR cc_start: 0.7095 (t80) cc_final: 0.6474 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 82
  average time/residue: 0.0716
  time to fit residues: 7.6521
Evaluate side-chains
  69 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue   99 GLU
Chi-restraints excluded: chain D residue  132 HIS
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  271 ASN
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  402 LEU
Chi-restraints excluded: chain F residue   46 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 54 optimal weight:   20.0000
   chunk 48 optimal weight:    7.9990
   chunk 51 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0980
   chunk 19 optimal weight:    2.9990
   overall best weight:    3.4188

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

Flipped N/Q/H residues before XYZ refinement:
D 126 ASN
D 271 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.160233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.128653 restraints weight = 7237.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.128189 restraints weight = 15139.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.129403 restraints weight = 13361.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.130180 restraints weight = 8436.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.130604 restraints weight = 7619.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   4775  Z= 0.176
  Angle     :  0.689  14.698   6467  Z= 0.371
  Chirality :  0.044   0.212    746
  Planarity :  0.006   0.125    834
  Dihedral  :  5.074  33.172    633
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  6.70 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.84 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.35), residues: 582
  helix:  0.99 (0.31), residues: 269
  sheet: -0.29 (0.49), residues: 122
  loop : -2.35 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 272 
 TYR   0.016   0.002   TYR D 140 
 PHE   0.023   0.002   PHE D 162 
 TRP   0.013   0.001   TRP D 299 
 HIS   0.004   0.001   HIS F   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 4775)
  covalent geometry    : angle       0.68923 ( 6467)
  hydrogen bonds       : bond        0.06512 (  224)
  hydrogen bonds       : angle       4.60739 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.191 
Fit side-chains
REVERT: D   80 ASN cc_start: 0.7823 (p0) cc_final: 0.7554 (p0)
REVERT: B   43 TYR cc_start: 0.7204 (t80) cc_final: 0.6534 (t80)
  outliers start: 18
  outliers final: 10
  residues processed: 88
  average time/residue: 0.0499
  time to fit residues: 6.1024
Evaluate side-chains
  76 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   99 GLU
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  402 LEU
Chi-restraints excluded: chain F residue   46 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 31 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 38 optimal weight:    0.0030
   overall best weight:    2.7998

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

Flipped N/Q/H residues before XYZ refinement:
D 126 ASN
D 271 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.160661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.129629 restraints weight = 7067.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.126057 restraints weight = 13219.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.127572 restraints weight = 12648.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.128360 restraints weight = 7871.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.128697 restraints weight = 6902.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.5099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   4775  Z= 0.165
  Angle     :  0.697  16.021   6467  Z= 0.374
  Chirality :  0.044   0.232    746
  Planarity :  0.006   0.124    834
  Dihedral  :  5.036  33.062    633
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  6.36 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.61 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    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: -0.36 (0.36), residues: 582
  helix:  1.13 (0.32), residues: 267
  sheet: -0.21 (0.50), residues: 122
  loop : -2.21 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 239 
 TYR   0.015   0.001   TYR D 140 
 PHE   0.020   0.001   PHE D 162 
 TRP   0.009   0.001   TRP D 299 
 HIS   0.003   0.001   HIS F   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4775)
  covalent geometry    : angle       0.69685 ( 6467)
  hydrogen bonds       : bond        0.06281 (  224)
  hydrogen bonds       : angle       4.66938 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.190 
Fit side-chains
REVERT: D   19 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6473 (m-30)
REVERT: D   80 ASN cc_start: 0.7872 (p0) cc_final: 0.7661 (p0)
REVERT: D  168 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8045 (t0)
REVERT: D  415 LYS cc_start: 0.8286 (mmmm) cc_final: 0.7778 (mttt)
REVERT: B   43 TYR cc_start: 0.7271 (t80) cc_final: 0.6577 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 80
  average time/residue: 0.0640
  time to fit residues: 6.8660
Evaluate side-chains
  75 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue   19 ASP
Chi-restraints excluded: chain D residue   99 GLU
Chi-restraints excluded: chain D residue  132 HIS
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  168 ASN
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  271 ASN
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain F residue   27 GLU
Chi-restraints excluded: chain F residue   46 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 42 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    0.2980
   chunk 25 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 39 optimal weight:   40.0000
   chunk 33 optimal weight:   10.0000
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
D 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.161361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.130854 restraints weight = 7240.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.129798 restraints weight = 15422.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.130734 restraints weight = 12376.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.130698 restraints weight = 8187.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.130993 restraints weight = 7879.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.5228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   4775  Z= 0.152
  Angle     :  0.682  14.885   6467  Z= 0.368
  Chirality :  0.044   0.251    746
  Planarity :  0.006   0.123    834
  Dihedral  :  4.915  32.800    633
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  6.19 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.80 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    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: -0.28 (0.36), residues: 582
  helix:  1.19 (0.32), residues: 267
  sheet: -0.17 (0.51), residues: 122
  loop : -2.19 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 272 
 TYR   0.015   0.001   TYR D 140 
 PHE   0.019   0.001   PHE D 162 
 TRP   0.009   0.001   TRP D 299 
 HIS   0.003   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4775)
  covalent geometry    : angle       0.68217 ( 6467)
  hydrogen bonds       : bond        0.06036 (  224)
  hydrogen bonds       : angle       4.64836 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.186 
Fit side-chains
REVERT: D   19 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.6015 (m-30)
REVERT: D  168 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.7986 (t0)
REVERT: D  415 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7772 (mttt)
REVERT: F   22 GLN cc_start: 0.5727 (pp30) cc_final: 0.5271 (tp-100)
REVERT: B   43 TYR cc_start: 0.7255 (t80) cc_final: 0.6556 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0607
  time to fit residues: 6.6309
Evaluate side-chains
  78 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue   19 ASP
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   86 PHE
Chi-restraints excluded: chain D residue   99 GLU
Chi-restraints excluded: chain D residue  132 HIS
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  168 ASN
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  271 ASN
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain F residue   46 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 7 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 57 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    4.2788

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

Flipped N/Q/H residues before XYZ refinement:
D 271 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.158343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127540 restraints weight = 7172.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.128160 restraints weight = 14528.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.129386 restraints weight = 12271.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.128559 restraints weight = 8020.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128940 restraints weight = 7941.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.5465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   4775  Z= 0.204
  Angle     :  0.737  14.218   6467  Z= 0.400
  Chirality :  0.045   0.263    746
  Planarity :  0.006   0.124    834
  Dihedral  :  5.123  33.833    633
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  7.04 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.42 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.36), residues: 582
  helix:  1.05 (0.32), residues: 267
  sheet: -0.39 (0.50), residues: 123
  loop : -2.23 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 272 
 TYR   0.015   0.002   TYR D 140 
 PHE   0.025   0.002   PHE D 162 
 TRP   0.016   0.001   TRP D 299 
 HIS   0.004   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 4775)
  covalent geometry    : angle       0.73659 ( 6467)
  hydrogen bonds       : bond        0.06714 (  224)
  hydrogen bonds       : angle       4.74153 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.206 
Fit side-chains
REVERT: D   19 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6649 (m-30)
REVERT: D  415 LYS cc_start: 0.8331 (mmmm) cc_final: 0.7840 (mttt)
REVERT: B   43 TYR cc_start: 0.7319 (t80) cc_final: 0.6586 (t80)
  outliers start: 17
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0785
  time to fit residues: 8.6970
Evaluate side-chains
  82 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue   19 ASP
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   99 GLU
Chi-restraints excluded: chain D residue  132 HIS
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  271 ASN
Chi-restraints excluded: chain D residue  279 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  342 VAL
Chi-restraints excluded: chain F residue   46 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0970
   chunk 36 optimal weight:    9.9990
   chunk 1 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 49 optimal weight:   20.0000
   chunk 0 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 35 optimal weight:   20.0000
   overall best weight:    3.1384

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

Flipped N/Q/H residues before XYZ refinement:
D 271 ASN
F  22 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.159335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.126645 restraints weight = 7206.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.121837 restraints weight = 10697.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.123322 restraints weight = 12069.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.124222 restraints weight = 7414.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.124884 restraints weight = 6294.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.5585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   4775  Z= 0.174
  Angle     :  0.728  13.868   6467  Z= 0.397
  Chirality :  0.045   0.274    746
  Planarity :  0.006   0.124    834
  Dihedral  :  5.029  33.704    633
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  6.36 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 24.18 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    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: -0.42 (0.36), residues: 582
  helix:  1.08 (0.32), residues: 268
  sheet: -0.36 (0.50), residues: 123
  loop : -2.18 (0.43), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 136 
 TYR   0.015   0.001   TYR D 140 
 PHE   0.020   0.001   PHE D 162 
 TRP   0.011   0.001   TRP D 299 
 HIS   0.003   0.001   HIS D 307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 4775)
  covalent geometry    : angle       0.72795 ( 6467)
  hydrogen bonds       : bond        0.06402 (  224)
  hydrogen bonds       : angle       4.70644 (  654)

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

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

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1164 Ramachandran restraints generated.
    582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.186 
Fit side-chains
REVERT: D   19 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6647 (m-30)
REVERT: D  415 LYS cc_start: 0.8315 (mmmm) cc_final: 0.7844 (mttt)
REVERT: B   17 ASP cc_start: 0.7779 (m-30) cc_final: 0.7496 (t0)
REVERT: B   43 TYR cc_start: 0.7512 (t80) cc_final: 0.6628 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 78
  average time/residue: 0.0714
  time to fit residues: 7.3054
Evaluate side-chains
  75 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    3 ILE
Chi-restraints excluded: chain D residue   19 ASP
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   99 GLU
Chi-restraints excluded: chain D residue  132 HIS
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  165 SER
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  271 ASN
Chi-restraints excluded: chain D residue  279 VAL
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  304 ASP
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain F residue   46 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    0.3980
   chunk 10 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 27 optimal weight:    4.9990
   chunk 37 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   overall best weight:    3.8788

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

Flipped N/Q/H residues before XYZ refinement:
D 271 ASN
F  22 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.158397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.125332 restraints weight = 7183.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.124059 restraints weight = 16721.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.125913 restraints weight = 13382.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.126108 restraints weight = 7771.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.126380 restraints weight = 7725.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.5693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   4775  Z= 0.195
  Angle     :  0.743  13.528   6467  Z= 0.400
  Chirality :  0.046   0.271    746
  Planarity :  0.006   0.124    834
  Dihedral  :  5.086  34.092    633
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  1.03 %
    Allowed  :  7.39 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 24.38 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    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: -0.54 (0.36), residues: 582
  helix:  0.99 (0.32), residues: 268
  sheet: -0.45 (0.50), residues: 123
  loop : -2.23 (0.43), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 272 
 TYR   0.015   0.001   TYR D 140 
 PHE   0.023   0.002   PHE D 162 
 TRP   0.013   0.001   TRP D 299 
 HIS   0.003   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 4775)
  covalent geometry    : angle       0.74318 ( 6467)
  hydrogen bonds       : bond        0.06639 (  224)
  hydrogen bonds       : angle       4.77315 (  654)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 979.08 seconds
wall clock time: 17 minutes 36.23 seconds (1056.23 seconds total)