Starting phenix.real_space_refine
on Thu Aug  6 10:48:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vxi_65409/08_2026/9vxi_65409.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vxi_65409/08_2026/9vxi_65409.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vxi_65409/08_2026/9vxi_65409.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vxi_65409/08_2026/9vxi_65409.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vxi_65409/08_2026/9vxi_65409.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vxi_65409/08_2026/9vxi_65409.map"
  }
  resolution = 2.47
  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=   0.049
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8021 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     Co      4      6.85       5
     P       4      5.49       5
     S      32      5.16       5
     C    5182      2.51       5
     N    1364      2.21       5
     O    1604      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8190
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2508
          Classifications: {'peptide': 325}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 318}
    Chain: "B"
      Number of atoms: 1556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1556
          Classifications: {'peptide': 197}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 190}
    Chain: "C"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 325, 2508
          Classifications: {'peptide': 325}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 318}
    Chain: "D"
      Number of atoms: 1556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1556
          Classifications: {'peptide': 197}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 190}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 31
          Unusual residues: {' CO': 2, 'GGS': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 31
          Unusual residues: {' CO': 2, 'GGS': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.08, per 1000 atoms: 0.25
  Number of scatterers: 8190
  At special positions: 0
  Unit cell: (97.572, 106.568, 94.112, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Co      4     26.99
     S      32     16.00
     P       4     15.00
     O    1604      8.00
     N    1364      7.00
     C    5182      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: 1.05
  Conformation dependent library (CDL) restraints added in 324.3 milliseconds
  

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      66.1% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 97
      removed outlier: 3.704A  pdb=" N   LEU A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 114
    Processing helix  chain 'A' and resid 118 through 129
    Processing helix  chain 'A' and resid 135 through 153
    Processing helix  chain 'A' and resid 158 through 182
      removed outlier: 3.562A  pdb=" N   GLN A 162 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 199
    Processing helix  chain 'A' and resid 199 through 222
      removed outlier: 3.898A  pdb=" N   GLU A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 247
    Processing helix  chain 'A' and resid 254 through 266
    Processing helix  chain 'A' and resid 266 through 282
      removed outlier: 3.757A  pdb=" N   ILE A 270 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 313
      removed outlier: 4.180A  pdb=" N   PHE A 311 " --> pdb=" O   ASP A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 328
      removed outlier: 3.583A  pdb=" N   LYS A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 339
    Processing helix  chain 'A' and resid 343 through 351
    Processing helix  chain 'A' and resid 357 through 369
    Processing helix  chain 'A' and resid 370 through 390
      removed outlier: 3.543A  pdb=" N   ARG A 374 " --> pdb=" O   GLY A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 396 through 412
    Processing helix  chain 'B' and resid 83 through 96
    Processing helix  chain 'B' and resid 99 through 103
    Processing helix  chain 'B' and resid 107 through 124
    Processing helix  chain 'B' and resid 129 through 132
      removed outlier: 3.773A  pdb=" N   ASP B 132 " --> pdb=" O   GLU B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 129 through 132'
    Processing helix  chain 'B' and resid 133 through 138
    Processing helix  chain 'B' and resid 153 through 159
    Processing helix  chain 'B' and resid 224 through 232
    Processing helix  chain 'B' and resid 234 through 243
    Processing helix  chain 'C' and resid 91 through 97
      removed outlier: 3.685A  pdb=" N   LEU C  95 " --> pdb=" O   SER C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 114
    Processing helix  chain 'C' and resid 118 through 129
    Processing helix  chain 'C' and resid 135 through 153
    Processing helix  chain 'C' and resid 158 through 182
      removed outlier: 3.564A  pdb=" N   GLN C 162 " --> pdb=" O   THR C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 199
    Processing helix  chain 'C' and resid 199 through 222
      removed outlier: 3.898A  pdb=" N   GLU C 222 " --> pdb=" O   LEU C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 247
    Processing helix  chain 'C' and resid 254 through 266
    Processing helix  chain 'C' and resid 266 through 282
      removed outlier: 3.759A  pdb=" N   ILE C 270 " --> pdb=" O   THR C 266 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 313
      removed outlier: 4.086A  pdb=" N   PHE C 311 " --> pdb=" O   ASP C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 328
      removed outlier: 3.614A  pdb=" N   LYS C 328 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 339
    Processing helix  chain 'C' and resid 343 through 351
    Processing helix  chain 'C' and resid 357 through 369
    Processing helix  chain 'C' and resid 370 through 390
      removed outlier: 3.543A  pdb=" N   ARG C 374 " --> pdb=" O   GLY C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 393
      No H-bonds generated for 'chain 'C' and resid 391 through 393'
    Processing helix  chain 'C' and resid 396 through 412
    Processing helix  chain 'D' and resid 83 through 96
    Processing helix  chain 'D' and resid 99 through 103
    Processing helix  chain 'D' and resid 107 through 124
    Processing helix  chain 'D' and resid 129 through 132
      removed outlier: 4.043A  pdb=" N   ASP D 132 " --> pdb=" O   GLU D 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 129 through 132'
    Processing helix  chain 'D' and resid 133 through 138
    Processing helix  chain 'D' and resid 153 through 159
    Processing helix  chain 'D' and resid 224 through 232
    Processing helix  chain 'D' and resid 234 through 243
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188
      removed outlier: 3.711A  pdb=" N   LYS A 191 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 142 through 147
      removed outlier: 5.313A  pdb=" N   PHE B 170 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 10.508A  pdb=" N   TYR B 146 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
      removed outlier: 14.002A  pdb=" N   GLY B 168 " --> pdb=" O   TYR B 146 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   LEU B 167 " --> pdb=" O   SER B 188 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   SER B 188 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASP B 169 " --> pdb=" O   LYS B 186 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   SER B 204 " --> pdb=" O   LEU B 217 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   LEU B 217 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   LYS B 206 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   ILE B 215 " --> pdb=" O   LYS B 206 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   THR B 208 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   VAL B 213 " --> pdb=" O   THR B 208 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   GLU B 271 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   LEU B 144 " --> pdb=" O   GLU B 271 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 187 through 188
      removed outlier: 3.707A  pdb=" N   LYS C 191 " --> pdb=" O   ARG C 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 142 through 147
      removed outlier: 5.304A  pdb=" N   PHE D 170 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
      removed outlier: 10.481A  pdb=" N   TYR D 146 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
      removed outlier: 14.007A  pdb=" N   GLY D 168 " --> pdb=" O   TYR D 146 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   LEU D 167 " --> pdb=" O   SER D 188 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   SER D 188 " --> pdb=" O   LEU D 167 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ASP D 169 " --> pdb=" O   LYS D 186 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   SER D 204 " --> pdb=" O   LEU D 217 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   LEU D 217 " --> pdb=" O   SER D 204 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   LYS D 206 " --> pdb=" O   ILE D 215 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   ILE D 215 " --> pdb=" O   LYS D 206 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   ILE D 250 " --> pdb=" O   ARG D 261 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ARG D 261 " --> pdb=" O   ILE D 250 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   GLU D 271 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   LEU D 144 " --> pdb=" O   GLU D 271 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1572 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.20 -     1.38: 3214
        1.38 -     1.56: 5022
        1.56 -     1.74: 6
        1.74 -     1.91: 52
        1.91 -     2.09: 2
  Bond restraints: 8296
  Sorted by residual:
  bond pdb=" O3A GGS A 501 "
       pdb=" PB  GGS A 501 "
    ideal  model  delta    sigma   weight residual
    1.760  1.617  0.143 2.00e-02 2.50e+03 5.10e+01
  bond pdb=" O3A GGS C 501 "
       pdb=" PB  GGS C 501 "
    ideal  model  delta    sigma   weight residual
    1.760  1.618  0.142 2.00e-02 2.50e+03 5.01e+01
  bond pdb=" PA  GGS C 501 "
       pdb=" S1  GGS C 501 "
    ideal  model  delta    sigma   weight residual
    2.170  2.092  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" PA  GGS A 501 "
       pdb=" S1  GGS A 501 "
    ideal  model  delta    sigma   weight residual
    2.170  2.092  0.078 2.00e-02 2.50e+03 1.53e+01
  bond pdb=" CG  LEU A 106 "
       pdb=" CD1 LEU A 106 "
    ideal  model  delta    sigma   weight residual
    1.521  1.401  0.120 3.30e-02 9.18e+02 1.32e+01
  ... (remaining 8291 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 10617
        2.24 -     4.48: 493
        4.48 -     6.72: 61
        6.72 -     8.96: 27
        8.96 -    11.20: 6
  Bond angle restraints: 11204
  Sorted by residual:
  angle pdb=" C   VAL C 114 "
        pdb=" N   GLY C 115 "
        pdb=" CA  GLY C 115 "
      ideal   model   delta    sigma   weight residual
     121.41  113.46    7.95 1.96e+00 2.60e-01 1.65e+01
  angle pdb=" C   VAL A 114 "
        pdb=" N   GLY A 115 "
        pdb=" CA  GLY A 115 "
      ideal   model   delta    sigma   weight residual
     121.41  113.71    7.70 1.96e+00 2.60e-01 1.54e+01
  angle pdb=" O1A GGS C 501 "
        pdb=" PA  GGS C 501 "
        pdb=" S1  GGS C 501 "
      ideal   model   delta    sigma   weight residual
     101.12  112.32  -11.20 3.00e+00 1.11e-01 1.39e+01
  angle pdb=" O1A GGS A 501 "
        pdb=" PA  GGS A 501 "
        pdb=" S1  GGS A 501 "
      ideal   model   delta    sigma   weight residual
     101.12  112.32  -11.20 3.00e+00 1.11e-01 1.39e+01
  angle pdb=" CA  TYR B 252 "
        pdb=" CB  TYR B 252 "
        pdb=" CG  TYR B 252 "
      ideal   model   delta    sigma   weight residual
     113.90  107.71    6.19 1.80e+00 3.09e-01 1.18e+01
  ... (remaining 11199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.87: 4909
       30.87 -    61.74: 166
       61.74 -    92.61: 15
       92.61 -   123.48: 0
      123.48 -   154.36: 4
  Dihedral angle restraints: 5094
    sinusoidal: 2062
      harmonic: 3032
  Sorted by residual:
  dihedral pdb=" O1A GGS C 501 "
           pdb=" O3A GGS C 501 "
           pdb=" PA  GGS C 501 "
           pdb=" PB  GGS C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -135.55   18.81 -154.36     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" O1A GGS A 501 "
           pdb=" O3A GGS A 501 "
           pdb=" PA  GGS A 501 "
           pdb=" PB  GGS A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -135.55   18.77 -154.32     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" CA  GLU D 129 "
           pdb=" C   GLU D 129 "
           pdb=" N   PRO D 130 "
           pdb=" CA  PRO D 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.80  -22.20     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 5091 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 739
       0.056 -    0.113: 450
       0.113 -    0.169: 91
       0.169 -    0.225: 26
       0.225 -    0.281: 6
  Chirality restraints: 1312
  Sorted by residual:
  chirality pdb=" CG  LEU A 269 "
            pdb=" CB  LEU A 269 "
            pdb=" CD1 LEU A 269 "
            pdb=" CD2 LEU A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CG  LEU C 269 "
            pdb=" CB  LEU C 269 "
            pdb=" CD1 LEU C 269 "
            pdb=" CD2 LEU C 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CB  VAL A 335 "
            pdb=" CA  VAL A 335 "
            pdb=" CG1 VAL A 335 "
            pdb=" CG2 VAL A 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 1309 not shown)

  Planarity restraints: 1438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 294 "    0.041 2.00e-02 2.50e+03   2.15e-02 9.21e+00
        pdb=" CG  TYR A 294 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 294 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 294 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 294 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 294 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 294 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A 294 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 294 "    0.041 2.00e-02 2.50e+03   2.14e-02 9.12e+00
        pdb=" CG  TYR C 294 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 294 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 294 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 294 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 294 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 294 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR C 294 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 146 "   -0.028 2.00e-02 2.50e+03   1.42e-02 4.06e+00
        pdb=" CG  TYR D 146 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 146 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 146 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 146 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 146 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 146 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR D 146 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1435 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.28: 23
        2.28 -     2.94: 3772
        2.94 -     3.59: 12604
        3.59 -     4.25: 21233
        4.25 -     4.90: 35139
  Nonbonded interactions: 72771
  Sorted by model distance:
  nonbonded pdb=" O1B GGS A 501 "
            pdb="CO    CO A 503 "
     model   vdw
     1.626 2.220
  nonbonded pdb=" O1B GGS C 501 "
            pdb="CO    CO C 502 "
     model   vdw
     1.627 2.220
  nonbonded pdb=" O1A GGS C 501 "
            pdb="CO    CO C 503 "
     model   vdw
     1.839 2.220
  nonbonded pdb=" O1A GGS A 501 "
            pdb="CO    CO A 502 "
     model   vdw
     1.842 2.220
  nonbonded pdb=" OH  TYR C 258 "
            pdb=" OD2 ASP C 307 "
     model   vdw
     1.920 3.040
  ... (remaining 72766 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.590
  Find NCS groups from input model:        0.150
  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:             0.000
  Load rotamer database and sin/cos tables:6.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
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      :  0.019   0.143   8296  Z= 0.807
  Angle     :  1.123  11.203  11204  Z= 0.588
  Chirality :  0.071   0.281   1312
  Planarity :  0.005   0.040   1438
  Dihedral  : 15.782 154.355   3126
  Min Nonbonded Distance : 1.626

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.22 (0.23), residues: 1036
  helix: -1.83 (0.16), residues: 654
  sheet: -2.75 (0.36), residues: 148
  loop : -1.75 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 296 
 TYR   0.041   0.006   TYR A 294 
 PHE   0.026   0.004   PHE A 129 
 TRP   0.013   0.004   TRP C 216 
 HIS   0.008   0.003   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01895 /  0.81 ( 8296)
  covalent geometry    : angle       1.12286 /  0.59 (11204)
  hydrogen bonds       : bond        0.13067 /  8.54 (  532)
  hydrogen bonds       : angle       7.02360 /  5.11 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  373 LYS cc_start: 0.7138 (mmtm) cc_final: 0.6783 (ttpt)
REVERT: B  122 GLU cc_start: 0.7453 (pp20) cc_final: 0.7037 (pp20)
REVERT: B  139 ASP cc_start: 0.7622 (t0) cc_final: 0.7213 (t70)
REVERT: B  163 ASP cc_start: 0.7183 (p0) cc_final: 0.6963 (t0)
REVERT: B  175 ASP cc_start: 0.8019 (t70) cc_final: 0.7287 (t0)
REVERT: C  222 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7441 (mt-10)
REVERT: C  373 LYS cc_start: 0.7128 (mmtm) cc_final: 0.6766 (ttpt)
REVERT: D   99 MET cc_start: 0.8105 (mmp) cc_final: 0.7750 (mmm)
REVERT: D  122 GLU cc_start: 0.7401 (pp20) cc_final: 0.6889 (pp20)
REVERT: D  139 ASP cc_start: 0.7783 (t0) cc_final: 0.7286 (t70)
REVERT: D  163 ASP cc_start: 0.7212 (p0) cc_final: 0.6990 (t0)
REVERT: D  175 ASP cc_start: 0.7933 (t70) cc_final: 0.7401 (t0)
REVERT: D  249 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7810 (tm-30)
REVERT: D  277 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7310 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.6958
  time to fit residues: 109.6251
Evaluate side-chains
  118 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 GLN
A 213 GLN
B 266 ASN
C 127 GLN
C 213 GLN
D 266 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.189036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.135685 restraints weight = 8730.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.07
r_work: 0.3413 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8296  Z= 0.155
  Angle     :  0.551   5.218  11204  Z= 0.297
  Chirality :  0.041   0.135   1312
  Planarity :  0.004   0.034   1438
  Dihedral  : 11.500 114.551   1164
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 14.16 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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: -0.81 (0.25), residues: 1036
  helix:  0.26 (0.19), residues: 660
  sheet: -2.31 (0.40), residues: 146
  loop : -1.20 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 380 
 TYR   0.012   0.002   TYR C 294 
 PHE   0.011   0.001   PHE B 170 
 TRP   0.010   0.002   TRP D 247 
 HIS   0.006   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 ( 8296)
  covalent geometry    : angle       0.55091 /  0.30 (11204)
  hydrogen bonds       : bond        0.04611 /  3.11 (  532)
  hydrogen bonds       : angle       5.03116 /  3.72 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  160 GLU cc_start: 0.8133 (mp0) cc_final: 0.7824 (mt-10)
REVERT: A  189 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8107 (mtt180)
REVERT: A  328 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7636 (ttmm)
REVERT: A  373 LYS cc_start: 0.6920 (mmtm) cc_final: 0.6438 (ttpt)
REVERT: B  122 GLU cc_start: 0.7094 (pp20) cc_final: 0.6542 (pp20)
REVERT: B  139 ASP cc_start: 0.7294 (t0) cc_final: 0.6887 (t70)
REVERT: B  141 CYS cc_start: 0.7494 (t) cc_final: 0.7266 (t)
REVERT: B  163 ASP cc_start: 0.7461 (p0) cc_final: 0.6855 (t0)
REVERT: B  254 ASP cc_start: 0.7674 (t0) cc_final: 0.7238 (t0)
REVERT: C  160 GLU cc_start: 0.8135 (mp0) cc_final: 0.7827 (mt-10)
REVERT: C  328 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7649 (ttmm)
REVERT: C  373 LYS cc_start: 0.6906 (mmtm) cc_final: 0.6419 (ttpt)
REVERT: D  122 GLU cc_start: 0.7158 (pp20) cc_final: 0.6396 (pp20)
REVERT: D  139 ASP cc_start: 0.7378 (t0) cc_final: 0.6861 (t70)
REVERT: D  163 ASP cc_start: 0.7435 (p0) cc_final: 0.6852 (t0)
REVERT: D  177 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8248 (mmtm)
REVERT: D  178 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7878 (mp0)
REVERT: D  249 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7487 (tm-30)
  outliers start: 9
  outliers final: 3
  residues processed: 147
  average time/residue: 0.5878
  time to fit residues: 91.4610
Evaluate side-chains
  131 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 127
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain D residue  176 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0470
   chunk 16 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0870
   chunk 36 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.4056

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 109 ASN
C 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.192257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.138657 restraints weight = 8834.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.16
r_work: 0.3453 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8296  Z= 0.122
  Angle     :  0.489   5.326  11204  Z= 0.263
  Chirality :  0.039   0.131   1312
  Planarity :  0.003   0.029   1438
  Dihedral  : 10.101  89.829   1164
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.72 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.49 (0.26), residues: 1036
  helix:  1.34 (0.20), residues: 660
  sheet: -1.82 (0.41), residues: 142
  loop : -0.99 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 380 
 TYR   0.012   0.001   TYR C 294 
 PHE   0.010   0.001   PHE B 170 
 TRP   0.007   0.001   TRP B 247 
 HIS   0.005   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 8296)
  covalent geometry    : angle       0.48912 /  0.26 (11204)
  hydrogen bonds       : bond        0.03931 /  2.65 (  532)
  hydrogen bonds       : angle       4.56949 /  3.38 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7939 (mm-30)
REVERT: A  160 GLU cc_start: 0.8445 (mp0) cc_final: 0.8166 (mt-10)
REVERT: A  373 LYS cc_start: 0.7209 (mmtm) cc_final: 0.6739 (ttpt)
REVERT: A  390 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8041 (tp)
REVERT: B  122 GLU cc_start: 0.7102 (pp20) cc_final: 0.6600 (pp20)
REVERT: B  136 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7867 (p0)
REVERT: B  141 CYS cc_start: 0.7701 (t) cc_final: 0.7482 (t)
REVERT: B  163 ASP cc_start: 0.7501 (p0) cc_final: 0.6918 (t0)
REVERT: B  254 ASP cc_start: 0.7710 (t0) cc_final: 0.7352 (t0)
REVERT: C  117 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7872 (mm-30)
REVERT: C  160 GLU cc_start: 0.8440 (mp0) cc_final: 0.8171 (mt-10)
REVERT: C  373 LYS cc_start: 0.7203 (mmtm) cc_final: 0.6736 (ttpt)
REVERT: C  390 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8036 (tp)
REVERT: D   99 MET cc_start: 0.8204 (mmp) cc_final: 0.7913 (mmm)
REVERT: D  122 GLU cc_start: 0.7138 (pp20) cc_final: 0.6462 (pp20)
REVERT: D  139 ASP cc_start: 0.7592 (t0) cc_final: 0.7205 (t70)
REVERT: D  163 ASP cc_start: 0.7487 (p0) cc_final: 0.6932 (t0)
REVERT: D  177 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8241 (mmtm)
REVERT: D  178 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7859 (mp0)
REVERT: D  249 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7555 (tm-30)
  outliers start: 16
  outliers final: 2
  residues processed: 152
  average time/residue: 0.5230
  time to fit residues: 84.3832
Evaluate side-chains
  138 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 132
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  177 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 87 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 90 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0000
   overall best weight:    0.6584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 109 ASN
A 244 GLN
C 109 ASN
C 244 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.191022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.137937 restraints weight = 8864.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 2.05
r_work: 0.3435 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8296  Z= 0.135
  Angle     :  0.490   5.987  11204  Z= 0.260
  Chirality :  0.040   0.178   1312
  Planarity :  0.003   0.027   1438
  Dihedral  :  9.433  83.976   1164
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.96 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.27), residues: 1036
  helix:  1.66 (0.20), residues: 662
  sheet: -1.59 (0.42), residues: 142
  loop : -0.84 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 380 
 TYR   0.013   0.002   TYR C 294 
 PHE   0.011   0.001   PHE B 170 
 TRP   0.007   0.001   TRP D 247 
 HIS   0.005   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 8296)
  covalent geometry    : angle       0.49045 /  0.26 (11204)
  hydrogen bonds       : bond        0.03998 /  2.68 (  532)
  hydrogen bonds       : angle       4.44483 /  3.29 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7834 (mm-30)
REVERT: A  160 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7842 (mt-10)
REVERT: A  189 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8119 (mtt180)
REVERT: A  328 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7529 (ttmm)
REVERT: A  373 LYS cc_start: 0.6840 (mmtm) cc_final: 0.6349 (ttpt)
REVERT: B   99 MET cc_start: 0.7985 (mmp) cc_final: 0.7644 (mmm)
REVERT: B  122 GLU cc_start: 0.6980 (pp20) cc_final: 0.6364 (pp20)
REVERT: B  141 CYS cc_start: 0.7496 (t) cc_final: 0.7270 (t)
REVERT: B  163 ASP cc_start: 0.7368 (p0) cc_final: 0.6758 (t0)
REVERT: B  173 MET cc_start: 0.7676 (mpt) cc_final: 0.7470 (mpt)
REVERT: B  178 GLU cc_start: 0.8545 (mp0) cc_final: 0.8277 (pm20)
REVERT: B  254 ASP cc_start: 0.7548 (t0) cc_final: 0.6789 (t0)
REVERT: C  117 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7766 (mm-30)
REVERT: C  160 GLU cc_start: 0.8170 (mp0) cc_final: 0.7856 (mt-10)
REVERT: C  162 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7120 (mm-40)
REVERT: C  328 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7548 (ttmm)
REVERT: C  373 LYS cc_start: 0.6839 (mmtm) cc_final: 0.6347 (ttpt)
REVERT: D   99 MET cc_start: 0.8104 (mmp) cc_final: 0.7661 (mmm)
REVERT: D  122 GLU cc_start: 0.7055 (pp20) cc_final: 0.6409 (pp20)
REVERT: D  163 ASP cc_start: 0.7353 (p0) cc_final: 0.6747 (t0)
REVERT: D  178 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7807 (mp0)
REVERT: D  249 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7397 (tm-30)
  outliers start: 19
  outliers final: 5
  residues processed: 153
  average time/residue: 0.5413
  time to fit residues: 87.7056
Evaluate side-chains
  139 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  239 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 80 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 4 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   chunk 101 optimal weight:    6.9990
   chunk 53 optimal weight:    0.1980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 109 ASN
C 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.192752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.138880 restraints weight = 8839.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.16
r_work: 0.3454 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8296  Z= 0.123
  Angle     :  0.471   5.163  11204  Z= 0.250
  Chirality :  0.040   0.151   1312
  Planarity :  0.003   0.025   1438
  Dihedral  :  8.952  83.821   1164
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.75 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.19 (0.27), residues: 1036
  helix:  1.87 (0.20), residues: 662
  sheet: -1.46 (0.42), residues: 142
  loop : -0.77 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 162 
 TYR   0.010   0.001   TYR C 294 
 PHE   0.010   0.001   PHE B 170 
 TRP   0.007   0.001   TRP B 247 
 HIS   0.005   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 8296)
  covalent geometry    : angle       0.47079 /  0.25 (11204)
  hydrogen bonds       : bond        0.03751 /  2.52 (  532)
  hydrogen bonds       : angle       4.32647 /  3.21 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  117 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7951 (mm-30)
REVERT: A  160 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8132 (mt-10)
REVERT: A  189 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8107 (mtt180)
REVERT: A  328 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7665 (ttmm)
REVERT: A  373 LYS cc_start: 0.7207 (mmtm) cc_final: 0.6714 (ttpt)
REVERT: A  380 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7193 (mtp85)
REVERT: B   99 MET cc_start: 0.8096 (mmp) cc_final: 0.7761 (mmm)
REVERT: B  122 GLU cc_start: 0.7149 (pp20) cc_final: 0.6506 (pp20)
REVERT: B  141 CYS cc_start: 0.7748 (t) cc_final: 0.7481 (t)
REVERT: B  163 ASP cc_start: 0.7381 (p0) cc_final: 0.6862 (t0)
REVERT: C  117 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7922 (mm-30)
REVERT: C  160 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8157 (mt-10)
REVERT: C  162 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7407 (mm110)
REVERT: C  328 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7698 (ttmm)
REVERT: C  373 LYS cc_start: 0.7215 (mmtm) cc_final: 0.6722 (ttpt)
REVERT: D   99 MET cc_start: 0.8236 (mmp) cc_final: 0.7730 (mmm)
REVERT: D  122 GLU cc_start: 0.7205 (pp20) cc_final: 0.6518 (pp20)
REVERT: D  163 ASP cc_start: 0.7388 (p0) cc_final: 0.6880 (t0)
REVERT: D  173 MET cc_start: 0.7546 (mpt) cc_final: 0.7316 (mpt)
REVERT: D  177 LYS cc_start: 0.8328 (mmtm) cc_final: 0.7994 (mtmt)
REVERT: D  178 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7655 (mp0)
REVERT: D  249 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7395 (tm-30)
  outliers start: 21
  outliers final: 4
  residues processed: 151
  average time/residue: 0.5514
  time to fit residues: 87.9674
Evaluate side-chains
  133 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  189 ARG
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain C residue  160 GLU
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  239 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 66 optimal weight:    0.4980
   chunk 63 optimal weight:    0.5980
   chunk 89 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0270
   chunk 82 optimal weight:    0.7980
   chunk 100 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.4038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 109 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.194275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.140701 restraints weight = 8686.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.14
r_work: 0.3479 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8296  Z= 0.113
  Angle     :  0.471   6.572  11204  Z= 0.249
  Chirality :  0.039   0.176   1312
  Planarity :  0.003   0.024   1438
  Dihedral  :  8.556  83.716   1164
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 18.76 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.38 (0.27), residues: 1036
  helix:  2.05 (0.20), residues: 662
  sheet: -1.49 (0.41), residues: 142
  loop : -0.75 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 162 
 TYR   0.009   0.001   TYR C 294 
 PHE   0.009   0.001   PHE B 170 
 TRP   0.007   0.001   TRP B 247 
 HIS   0.005   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 ( 8296)
  covalent geometry    : angle       0.47064 /  0.25 (11204)
  hydrogen bonds       : bond        0.03553 /  2.41 (  532)
  hydrogen bonds       : angle       4.22067 /  3.13 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.8006 (mt) cc_final: 0.7747 (tp)
REVERT: A  160 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8128 (mt-10)
REVERT: A  162 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7383 (mm110)
REVERT: A  191 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7205 (mmpt)
REVERT: A  328 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7702 (ttmm)
REVERT: A  373 LYS cc_start: 0.7195 (mmtm) cc_final: 0.6706 (ttpt)
REVERT: A  380 ARG cc_start: 0.7707 (ttm110) cc_final: 0.7194 (mtp85)
REVERT: A  405 MET cc_start: 0.6637 (mtm) cc_final: 0.6422 (mtm)
REVERT: B   99 MET cc_start: 0.8093 (mmp) cc_final: 0.7766 (mmm)
REVERT: B  122 GLU cc_start: 0.7142 (pp20) cc_final: 0.6488 (pp20)
REVERT: B  141 CYS cc_start: 0.7695 (t) cc_final: 0.7421 (t)
REVERT: B  163 ASP cc_start: 0.7353 (p0) cc_final: 0.6836 (t0)
REVERT: C  160 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8153 (mt-10)
REVERT: C  162 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7430 (mm110)
REVERT: C  189 ARG cc_start: 0.8524 (mtp180) cc_final: 0.8250 (mtp85)
REVERT: C  191 LYS cc_start: 0.7806 (mtpp) cc_final: 0.7209 (mmpt)
REVERT: C  257 ASP cc_start: 0.8281 (t70) cc_final: 0.8077 (t70)
REVERT: C  328 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7707 (ttmm)
REVERT: C  373 LYS cc_start: 0.7224 (mmtm) cc_final: 0.6724 (ttpt)
REVERT: C  380 ARG cc_start: 0.7715 (ttm110) cc_final: 0.7209 (mtp85)
REVERT: D  122 GLU cc_start: 0.7188 (pp20) cc_final: 0.6497 (pp20)
REVERT: D  163 ASP cc_start: 0.7371 (p0) cc_final: 0.6890 (t0)
REVERT: D  173 MET cc_start: 0.7540 (mpt) cc_final: 0.7330 (mpt)
REVERT: D  177 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7878 (mtmt)
REVERT: D  178 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7678 (mp0)
REVERT: D  249 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7462 (tm-30)
  outliers start: 19
  outliers final: 4
  residues processed: 149
  average time/residue: 0.5009
  time to fit residues: 79.0040
Evaluate side-chains
  134 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain C residue  160 GLU
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  221 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0000
   chunk 88 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.6584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 109 ASN
C 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.192575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.138523 restraints weight = 8862.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.16
r_work: 0.3451 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8296  Z= 0.132
  Angle     :  0.489   8.314  11204  Z= 0.257
  Chirality :  0.040   0.224   1312
  Planarity :  0.003   0.024   1438
  Dihedral  :  8.338  83.520   1164
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.33 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.34 (0.27), residues: 1036
  helix:  2.02 (0.20), residues: 662
  sheet: -1.66 (0.39), residues: 146
  loop : -0.64 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 162 
 TYR   0.011   0.002   TYR C 294 
 PHE   0.011   0.001   PHE D 170 
 TRP   0.007   0.001   TRP B 247 
 HIS   0.005   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 8296)
  covalent geometry    : angle       0.48855 /  0.26 (11204)
  hydrogen bonds       : bond        0.03790 /  2.55 (  532)
  hydrogen bonds       : angle       4.26094 /  3.15 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.7987 (mt) cc_final: 0.7726 (tp)
REVERT: A  118 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6932 (t0)
REVERT: A  160 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8155 (mt-10)
REVERT: A  162 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7583 (mm110)
REVERT: A  191 LYS cc_start: 0.7787 (mtpp) cc_final: 0.7204 (mmpt)
REVERT: A  328 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7728 (ttmm)
REVERT: A  373 LYS cc_start: 0.7204 (mmtm) cc_final: 0.6713 (ttpt)
REVERT: A  380 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7209 (mtp85)
REVERT: A  388 GLN cc_start: 0.7444 (mm110) cc_final: 0.6705 (tp-100)
REVERT: B   99 MET cc_start: 0.8110 (mmp) cc_final: 0.7769 (mmm)
REVERT: B  122 GLU cc_start: 0.7171 (pp20) cc_final: 0.6502 (pp20)
REVERT: B  141 CYS cc_start: 0.7757 (t) cc_final: 0.7450 (t)
REVERT: B  163 ASP cc_start: 0.7358 (p0) cc_final: 0.6871 (t0)
REVERT: C  160 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8142 (mt-10)
REVERT: C  162 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7572 (mm110)
REVERT: C  189 ARG cc_start: 0.8473 (mtp180) cc_final: 0.8211 (mtp85)
REVERT: C  328 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7703 (ttmm)
REVERT: C  373 LYS cc_start: 0.7192 (mmtm) cc_final: 0.6692 (ttpt)
REVERT: C  380 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7233 (mtp85)
REVERT: C  388 GLN cc_start: 0.7484 (mm110) cc_final: 0.6768 (tp-100)
REVERT: D  122 GLU cc_start: 0.7196 (pp20) cc_final: 0.6503 (pp20)
REVERT: D  163 ASP cc_start: 0.7338 (p0) cc_final: 0.6881 (t0)
REVERT: D  177 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7930 (mtmt)
REVERT: D  178 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7727 (mp0)
REVERT: D  249 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7468 (tm-30)
REVERT: D  266 ASN cc_start: 0.8198 (m-40) cc_final: 0.7762 (t0)
  outliers start: 20
  outliers final: 8
  residues processed: 145
  average time/residue: 0.5590
  time to fit residues: 85.6881
Evaluate side-chains
  139 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  118 ASN
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain C residue  160 GLU
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  239 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0770
   chunk 91 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 98 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    0.6940

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.191565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.138392 restraints weight = 8752.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 2.03
r_work: 0.3443 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8296  Z= 0.136
  Angle     :  0.495   7.194  11204  Z= 0.259
  Chirality :  0.040   0.222   1312
  Planarity :  0.003   0.024   1438
  Dihedral  :  8.256  82.931   1164
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.89 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.33 (0.27), residues: 1036
  helix:  2.00 (0.20), residues: 662
  sheet: -1.55 (0.40), residues: 142
  loop : -0.71 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 162 
 TYR   0.011   0.002   TYR C 294 
 PHE   0.011   0.001   PHE B 170 
 TRP   0.007   0.001   TRP B 247 
 HIS   0.004   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 8296)
  covalent geometry    : angle       0.49504 /  0.26 (11204)
  hydrogen bonds       : bond        0.03805 /  2.57 (  532)
  hydrogen bonds       : angle       4.28329 /  3.17 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.7783 (mt) cc_final: 0.7579 (tp)
REVERT: A  118 ASN cc_start: 0.6895 (OUTLIER) cc_final: 0.6649 (t0)
REVERT: A  160 GLU cc_start: 0.8171 (mp0) cc_final: 0.7846 (mt-10)
REVERT: A  162 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7211 (mm110)
REVERT: A  328 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7556 (ttmm)
REVERT: A  373 LYS cc_start: 0.6841 (mmtm) cc_final: 0.6336 (ttpt)
REVERT: A  380 ARG cc_start: 0.7434 (ttm110) cc_final: 0.6827 (mtp85)
REVERT: A  388 GLN cc_start: 0.7186 (mm110) cc_final: 0.6372 (tp-100)
REVERT: B   99 MET cc_start: 0.7983 (mmp) cc_final: 0.7669 (mmm)
REVERT: B  122 GLU cc_start: 0.7094 (pp20) cc_final: 0.6430 (pp20)
REVERT: B  141 CYS cc_start: 0.7549 (t) cc_final: 0.7265 (t)
REVERT: B  163 ASP cc_start: 0.7201 (p0) cc_final: 0.6667 (t0)
REVERT: B  177 LYS cc_start: 0.8823 (mttp) cc_final: 0.8599 (mmtm)
REVERT: C  160 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7824 (mt-10)
REVERT: C  162 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7196 (mm110)
REVERT: C  189 ARG cc_start: 0.8476 (mtp180) cc_final: 0.8202 (mtp85)
REVERT: C  328 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7509 (ttmm)
REVERT: C  373 LYS cc_start: 0.6817 (mmtm) cc_final: 0.6303 (ttpt)
REVERT: C  380 ARG cc_start: 0.7450 (ttm110) cc_final: 0.6857 (mtp85)
REVERT: C  388 GLN cc_start: 0.7194 (mm110) cc_final: 0.6394 (tp-100)
REVERT: D  122 GLU cc_start: 0.7104 (pp20) cc_final: 0.6422 (pp20)
REVERT: D  163 ASP cc_start: 0.7196 (p0) cc_final: 0.6679 (t0)
REVERT: D  177 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7860 (mtmt)
REVERT: D  178 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7722 (mp0)
REVERT: D  249 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7325 (tm-30)
  outliers start: 20
  outliers final: 9
  residues processed: 144
  average time/residue: 0.5026
  time to fit residues: 76.5964
Evaluate side-chains
  141 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  118 ASN
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  160 GLU
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain D residue  176 VAL
Chi-restraints excluded: chain D residue  221 THR
Chi-restraints excluded: chain D residue  239 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0970
   chunk 86 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 109 ASN
C 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.192159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.139289 restraints weight = 8743.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.03
r_work: 0.3451 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8296  Z= 0.133
  Angle     :  0.503   7.944  11204  Z= 0.264
  Chirality :  0.040   0.202   1312
  Planarity :  0.003   0.024   1438
  Dihedral  :  8.160  82.406   1164
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.45 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.33 (0.27), residues: 1036
  helix:  2.01 (0.20), residues: 664
  sheet: -1.48 (0.41), residues: 138
  loop : -0.82 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 162 
 TYR   0.010   0.001   TYR C 294 
 PHE   0.011   0.001   PHE B 170 
 TRP   0.007   0.001   TRP B 247 
 HIS   0.004   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 ( 8296)
  covalent geometry    : angle       0.50252 /  0.26 (11204)
  hydrogen bonds       : bond        0.03732 /  2.52 (  532)
  hydrogen bonds       : angle       4.26891 /  3.17 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.7829 (mt) cc_final: 0.7604 (tp)
REVERT: A  160 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7832 (mt-10)
REVERT: A  162 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7209 (mm110)
REVERT: A  328 LYS cc_start: 0.7991 (ttpp) cc_final: 0.7507 (ttmm)
REVERT: A  373 LYS cc_start: 0.6844 (mmtm) cc_final: 0.6338 (ttpt)
REVERT: A  380 ARG cc_start: 0.7416 (ttm110) cc_final: 0.6813 (mtp85)
REVERT: A  388 GLN cc_start: 0.7186 (mm110) cc_final: 0.6382 (tp-100)
REVERT: B   99 MET cc_start: 0.7959 (mmp) cc_final: 0.7644 (mmm)
REVERT: B  122 GLU cc_start: 0.7048 (pp20) cc_final: 0.6378 (pp20)
REVERT: B  163 ASP cc_start: 0.7210 (p0) cc_final: 0.6675 (t0)
REVERT: B  173 MET cc_start: 0.7217 (mpt) cc_final: 0.6864 (mpt)
REVERT: C  160 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7814 (mt-10)
REVERT: C  162 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7182 (mm110)
REVERT: C  189 ARG cc_start: 0.8489 (mtp180) cc_final: 0.8221 (mtp85)
REVERT: C  257 ASP cc_start: 0.8110 (t70) cc_final: 0.7786 (t70)
REVERT: C  328 LYS cc_start: 0.8016 (ttpp) cc_final: 0.7525 (ttmm)
REVERT: C  373 LYS cc_start: 0.6777 (mmtm) cc_final: 0.6273 (ttpt)
REVERT: C  380 ARG cc_start: 0.7436 (ttm110) cc_final: 0.6848 (mtp85)
REVERT: C  388 GLN cc_start: 0.7205 (mm110) cc_final: 0.6402 (tp-100)
REVERT: D  122 GLU cc_start: 0.7078 (pp20) cc_final: 0.6392 (pp20)
REVERT: D  163 ASP cc_start: 0.7238 (p0) cc_final: 0.6707 (t0)
REVERT: D  249 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7290 (tm-30)
  outliers start: 20
  outliers final: 8
  residues processed: 136
  average time/residue: 0.5311
  time to fit residues: 76.7461
Evaluate side-chains
  137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  160 GLU
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain D residue  176 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0770
   chunk 85 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.7540

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 109 ASN
C 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.190505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.141761 restraints weight = 8749.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 1.76
r_work: 0.3453 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8296  Z= 0.146
  Angle     :  0.516   8.738  11204  Z= 0.270
  Chirality :  0.041   0.280   1312
  Planarity :  0.003   0.023   1438
  Dihedral  :  8.116  82.018   1164
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 21.24 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.26 (0.27), residues: 1036
  helix:  1.94 (0.20), residues: 664
  sheet: -1.46 (0.41), residues: 138
  loop : -0.83 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 368 
 TYR   0.011   0.002   TYR C 294 
 PHE   0.012   0.001   PHE B 170 
 TRP   0.007   0.001   TRP B 247 
 HIS   0.004   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.15 ( 8296)
  covalent geometry    : angle       0.51580 /  0.27 (11204)
  hydrogen bonds       : bond        0.03884 /  2.62 (  532)
  hydrogen bonds       : angle       4.31384 /  3.20 ( 1572)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.8010 (mt) cc_final: 0.7760 (tp)
REVERT: A  160 GLU cc_start: 0.8470 (mp0) cc_final: 0.8187 (mt-10)
REVERT: A  162 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7684 (mm110)
REVERT: A  328 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7753 (ttmm)
REVERT: A  373 LYS cc_start: 0.7298 (mmtm) cc_final: 0.6834 (ttpt)
REVERT: A  380 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7278 (mtp85)
REVERT: A  388 GLN cc_start: 0.7500 (mm110) cc_final: 0.6783 (tp-100)
REVERT: B   99 MET cc_start: 0.8129 (mmp) cc_final: 0.7843 (mmm)
REVERT: B  122 GLU cc_start: 0.7234 (pp20) cc_final: 0.6550 (pp20)
REVERT: B  163 ASP cc_start: 0.7324 (p0) cc_final: 0.6900 (t0)
REVERT: B  173 MET cc_start: 0.7610 (mpt) cc_final: 0.7267 (mpt)
REVERT: C  160 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8189 (mt-10)
REVERT: C  162 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7660 (mm110)
REVERT: C  189 ARG cc_start: 0.8596 (mtp180) cc_final: 0.8366 (mtp85)
REVERT: C  257 ASP cc_start: 0.8355 (t70) cc_final: 0.8104 (t70)
REVERT: C  328 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7753 (ttmm)
REVERT: C  373 LYS cc_start: 0.7242 (mmtm) cc_final: 0.6769 (ttpt)
REVERT: C  380 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7291 (mtp85)
REVERT: C  388 GLN cc_start: 0.7514 (mm110) cc_final: 0.6808 (tp-100)
REVERT: D  122 GLU cc_start: 0.7271 (pp20) cc_final: 0.6575 (pp20)
REVERT: D  163 ASP cc_start: 0.7321 (p0) cc_final: 0.6918 (t0)
REVERT: D  249 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7510 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 132
  average time/residue: 0.4980
  time to fit residues: 69.5410
Evaluate side-chains
  134 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  160 GLU
Chi-restraints excluded: chain C residue  162 GLN
Chi-restraints excluded: chain C residue  285 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain D residue  221 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0000
   overall best weight:    0.9590

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 109 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.189395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.141870 restraints weight = 8765.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 1.92
r_work: 0.3427 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8296  Z= 0.165
  Angle     :  0.537   8.228  11204  Z= 0.281
  Chirality :  0.041   0.256   1312
  Planarity :  0.003   0.024   1438
  Dihedral  :  8.133  81.332   1164
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 21.12 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  1.18 (0.27), residues: 1036
  helix:  1.85 (0.20), residues: 664
  sheet: -1.44 (0.41), residues: 138
  loop : -0.79 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 162 
 TYR   0.013   0.002   TYR C 294 
 PHE   0.014   0.001   PHE B 170 
 TRP   0.007   0.001   TRP B 247 
 HIS   0.004   0.001   HIS A 376 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.17 ( 8296)
  covalent geometry    : angle       0.53669 /  0.28 (11204)
  hydrogen bonds       : bond        0.04094 /  2.76 (  532)
  hydrogen bonds       : angle       4.39780 /  3.26 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3978.08 seconds
wall clock time: 68 minutes 9.32 seconds (4089.32 seconds total)