Starting phenix.real_space_refine
on Tue Feb  3 22:34:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i9k_52761/02_2026/9i9k_52761.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i9k_52761/02_2026/9i9k_52761.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i9k_52761/02_2026/9i9k_52761.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i9k_52761/02_2026/9i9k_52761.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i9k_52761/02_2026/9i9k_52761.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i9k_52761/02_2026/9i9k_52761.cif"
  }
  resolution = 2.4
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      4      5.21       5
     S      38      5.16       5
     C    4809      2.51       5
     N    1277      2.21       5
     O    1360      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7492
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "H"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 2266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2266
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 277, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 262}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 2402
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2402
          Classifications: {'peptide': 301}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 282}
    Chain: "K"
      Number of atoms: 2234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2234
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 17, 'TRANS': 258}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 2, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "K"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 2, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "I"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "J"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.47, per 1000 atoms: 0.20
  Number of scatterers: 7492
  At special positions: 0
  Unit cell: (79.002, 100.548, 105.678, 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)
     S      38     16.00
     P       4     15.00
     Mg      4     11.99
     O    1360      8.00
     N    1277      7.00
     C    4809      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 261.2 milliseconds
  

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 6 sheets defined
      55.0% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'H' and resid 262 through 266
    Processing helix  chain 'H' and resid 270 through 275
      removed outlier: 3.812A  pdb=" N   VAL H 275 " --> pdb=" O   LEU H 272 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 279 through 285
      removed outlier: 3.645A  pdb=" N   GLY H 285 " --> pdb=" O   GLN H 281 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 288 through 302
      removed outlier: 3.883A  pdb=" N   ALA H 292 " --> pdb=" O   THR H 288 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1 through 4
      removed outlier: 3.603A  pdb=" N   ASN I   4 " --> pdb=" O   MET I   1 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 1 through 4'
    Processing helix  chain 'I' and resid 5 through 11
    Processing helix  chain 'I' and resid 15 through 38
      removed outlier: 3.591A  pdb=" N   LEU I  19 " --> pdb=" O   SER I  15 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 49 through 70
    Processing helix  chain 'I' and resid 76 through 94
      removed outlier: 3.969A  pdb=" N   ASN I  93 " --> pdb=" O   ARG I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 116
    Processing helix  chain 'I' and resid 121 through 128
    Processing helix  chain 'I' and resid 134 through 154
      removed outlier: 4.746A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LEU I 149 " --> pdb=" O   GLU I 145 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 163 through 178
    Processing helix  chain 'I' and resid 183 through 186
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.501A  pdb=" N   THR I 201 " --> pdb=" O   ARG I 197 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 225
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.622A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 241 through 262
    Processing helix  chain 'I' and resid 266 through 281
    Processing helix  chain 'J' and resid 47 through 53
      removed outlier: 3.639A  pdb=" N   LYS J  52 " --> pdb=" O   ARG J  48 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASP J  53 " --> pdb=" O   SER J  49 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 56 through 67
    Processing helix  chain 'J' and resid 98 through 104
    Processing helix  chain 'J' and resid 110 through 131
      removed outlier: 3.512A  pdb=" N   HIS J 131 " --> pdb=" O   TYR J 127 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 139 through 141
      No H-bonds generated for 'chain 'J' and resid 139 through 141'
    Processing helix  chain 'J' and resid 175 through 179
    Processing helix  chain 'J' and resid 180 through 185
    Processing helix  chain 'J' and resid 192 through 209
    Processing helix  chain 'J' and resid 217 through 230
    Processing helix  chain 'J' and resid 239 through 243
    Processing helix  chain 'J' and resid 256 through 261
    Processing helix  chain 'J' and resid 265 through 276
    Processing helix  chain 'J' and resid 285 through 291
    Processing helix  chain 'J' and resid 292 through 297
      removed outlier: 3.897A  pdb=" N   SER J 296 " --> pdb=" O   MET J 292 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 303 through 307
    Processing helix  chain 'K' and resid 50 through 58
    Processing helix  chain 'K' and resid 87 through 94
    Processing helix  chain 'K' and resid 100 through 121
    Processing helix  chain 'K' and resid 129 through 131
      No H-bonds generated for 'chain 'K' and resid 129 through 131'
    Processing helix  chain 'K' and resid 170 through 175
    Processing helix  chain 'K' and resid 182 through 199
      removed outlier: 3.633A  pdb=" N   ILE K 186 " --> pdb=" O   THR K 182 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 207 through 220
    Processing helix  chain 'K' and resid 247 through 252
      removed outlier: 3.866A  pdb=" N   VAL K 251 " --> pdb=" O   ASP K 247 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 256 through 267
    Processing helix  chain 'K' and resid 276 through 282
      removed outlier: 3.612A  pdb=" N   ALA K 282 " --> pdb=" O   LYS K 278 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 283 through 289
      removed outlier: 4.531A  pdb=" N   ASP K 288 " --> pdb=" O   PHE K 285 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL K 289 " --> pdb=" O   PHE K 286 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'J' and resid 16 through 20
      removed outlier: 5.854A  pdb=" N   PHE J  17 " --> pdb=" O   LYS J  28 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   LYS J  28 " --> pdb=" O   PHE J  17 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ILE J  87 " --> pdb=" O   ILE J  43 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASP J  79 " --> pdb=" O   VAL J  90 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   LEU J  77 " --> pdb=" O   ASP J  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97
    Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134
    Processing sheet with id=AA4, first strand: chain 'K' and resid 5 through 11
      removed outlier: 5.312A  pdb=" N   LYS K   6 " --> pdb=" O   ARG K  22 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ARG K  22 " --> pdb=" O   LYS K   6 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL K  18 " --> pdb=" O   ILE K  10 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ASP K  68 " --> pdb=" O   VAL K  79 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   GLU K  81 " --> pdb=" O   LEU K  66 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   LEU K  66 " --> pdb=" O   GLU K  81 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'K' and resid 85 through 86
      removed outlier: 3.581A  pdb=" N   GLN K  85 " --> pdb=" O   ILE K 135 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 123 through 124

    362 hydrogen bonds defined for protein.
    1020 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.71

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2386
        1.34 -     1.46: 1576
        1.46 -     1.58: 3624
        1.58 -     1.70: 6
        1.70 -     1.81: 60
  Bond restraints: 7652
  Sorted by residual:
  bond pdb=" C   HIS I 161 "
       pdb=" N   ASN I 162 "
    ideal  model  delta    sigma   weight residual
    1.329  1.285  0.044 3.03e-02 1.09e+03 2.12e+00
  bond pdb=" C   ACE I   0 "
       pdb=" O   ACE I   0 "
    ideal  model  delta    sigma   weight residual
    1.199  1.226 -0.027 2.00e-02 2.50e+03 1.85e+00
  bond pdb=" C4  ADP K 301 "
       pdb=" C5  ADP K 301 "
    ideal  model  delta    sigma   weight residual
    1.490  1.465  0.025 2.00e-02 2.50e+03 1.53e+00
  bond pdb=" C4  ADP J 401 "
       pdb=" C5  ADP J 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.467  0.023 2.00e-02 2.50e+03 1.34e+00
  bond pdb=" C   LYS K  34 "
       pdb=" N   ILE K  35 "
    ideal  model  delta    sigma   weight residual
    1.330  1.308  0.022 1.97e-02 2.58e+03 1.22e+00
  ... (remaining 7647 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 10038
        1.59 -     3.19: 265
        3.19 -     4.78: 47
        4.78 -     6.37: 15
        6.37 -     7.97: 5
  Bond angle restraints: 10370
  Sorted by residual:
  angle pdb=" C   VAL I 259 "
        pdb=" N   LYS I 260 "
        pdb=" CA  LYS I 260 "
      ideal   model   delta    sigma   weight residual
     121.14  116.78    4.36 1.75e+00 3.27e-01 6.19e+00
  angle pdb=" C   HIS I 161 "
        pdb=" N   ASN I 162 "
        pdb=" CA  ASN I 162 "
      ideal   model   delta    sigma   weight residual
     121.98  129.62   -7.64 3.11e+00 1.03e-01 6.03e+00
  angle pdb=" O1B ADP K 301 "
        pdb=" PB  ADP K 301 "
        pdb=" O2B ADP K 301 "
      ideal   model   delta    sigma   weight residual
     119.90  112.61    7.29 3.00e+00 1.11e-01 5.90e+00
  angle pdb=" CA  LEU K 166 "
        pdb=" CB  LEU K 166 "
        pdb=" CG  LEU K 166 "
      ideal   model   delta    sigma   weight residual
     116.30  124.27   -7.97 3.50e+00 8.16e-02 5.18e+00
  angle pdb=" C1' ADP K 301 "
        pdb=" C2' ADP K 301 "
        pdb=" C3' ADP K 301 "
      ideal   model   delta    sigma   weight residual
     111.00  104.44    6.56 3.00e+00 1.11e-01 4.79e+00
  ... (remaining 10365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.38: 4267
       25.38 -    50.77: 302
       50.77 -    76.15: 36
       76.15 -   101.53: 5
      101.53 -   126.92: 1
  Dihedral angle restraints: 4611
    sinusoidal: 1919
      harmonic: 2692
  Sorted by residual:
  dihedral pdb=" C5' ADP J 401 "
           pdb=" O5' ADP J 401 "
           pdb=" PA  ADP J 401 "
           pdb=" O2A ADP J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   66.92 -126.92     1      2.00e+01 2.50e-03 3.84e+01
  dihedral pdb=" O1B ADP K 301 "
           pdb=" O3A ADP K 301 "
           pdb=" PB  ADP K 301 "
           pdb=" PA  ADP K 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -159.20   99.20     1      2.00e+01 2.50e-03 2.78e+01
  dihedral pdb=" CA  TYR K  19 "
           pdb=" C   TYR K  19 "
           pdb=" N   LYS K  20 "
           pdb=" CA  LYS K  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.48   19.52     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 4608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 643
       0.031 -    0.063: 332
       0.063 -    0.094: 109
       0.094 -    0.126: 55
       0.126 -    0.157: 7
  Chirality restraints: 1146
  Sorted by residual:
  chirality pdb=" CA  PRO J 238 "
            pdb=" N   PRO J 238 "
            pdb=" C   PRO J 238 "
            pdb=" CB  PRO J 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.16e-01
  chirality pdb=" CG  LEU K  83 "
            pdb=" CB  LEU K  83 "
            pdb=" CD1 LEU K  83 "
            pdb=" CD2 LEU K  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.78e-01
  chirality pdb=" CA  VAL H 260 "
            pdb=" N   VAL H 260 "
            pdb=" C   VAL H 260 "
            pdb=" CB  VAL H 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.53e-01
  ... (remaining 1143 not shown)

  Planarity restraints: 1313
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE K 193 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.28e+00
        pdb=" C   PHE K 193 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   PHE K 193 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA K 194 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K 291 "    0.028 5.00e-02 4.00e+02   4.24e-02 2.88e+00
        pdb=" N   PRO K 292 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO K 292 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO K 292 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN H 249 "    0.008 2.00e-02 2.50e+03   1.56e-02 2.44e+00
        pdb=" CD  GLN H 249 "   -0.027 2.00e-02 2.50e+03
        pdb=" OE1 GLN H 249 "    0.010 2.00e-02 2.50e+03
        pdb=" NE2 GLN H 249 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1310 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 33
        2.49 -     3.09: 5114
        3.09 -     3.70: 11352
        3.70 -     4.30: 17457
        4.30 -     4.90: 28103
  Nonbonded interactions: 62059
  Sorted by model distance:
  nonbonded pdb=" O3B ADP K 301 "
            pdb="MG    MG K 302 "
     model   vdw
     1.889 2.170
  nonbonded pdb=" O2A ADP J 401 "
            pdb="MG    MG J 402 "
     model   vdw
     1.910 2.170
  nonbonded pdb=" OD1 ASP K 145 "
            pdb="MG    MG K 302 "
     model   vdw
     1.921 2.170
  nonbonded pdb=" OD2 ASP K 145 "
            pdb="MG    MG K 303 "
     model   vdw
     1.971 2.170
  nonbonded pdb=" O1B ADP K 301 "
            pdb="MG    MG K 303 "
     model   vdw
     1.985 2.170
  ... (remaining 62054 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.610
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7652  Z= 0.194
  Angle     :  0.678   7.966  10370  Z= 0.349
  Chirality :  0.044   0.157   1146
  Planarity :  0.005   0.042   1313
  Dihedral  : 16.783 126.918   2867
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 23.11 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  0.83 (0.27), residues: 903
  helix:  1.57 (0.25), residues: 437
  sheet: -0.93 (0.56), residues: 56
  loop : -0.30 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 157 
 TYR   0.013   0.002   TYR I  91 
 PHE   0.018   0.002   PHE H 305 
 TRP   0.011   0.002   TRP J 237 
 HIS   0.007   0.001   HIS J  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 7652)
  covalent geometry    : angle       0.67754 (10370)
  hydrogen bonds       : bond        0.14388 (  362)
  hydrogen bonds       : angle       5.59705 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.196 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 113
  average time/residue: 0.6039
  time to fit residues: 71.4548
Evaluate side-chains
  111 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   34 THR
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  292 MET
Chi-restraints excluded: chain K residue   69 VAL
Chi-restraints excluded: chain K residue  160 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
K 121 HIS
K 131 GLN
K 268 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.135645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.109401 restraints weight = 9445.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.98
r_work: 0.3240 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.0770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7652  Z= 0.113
  Angle     :  0.555   7.747  10370  Z= 0.269
  Chirality :  0.042   0.132   1146
  Planarity :  0.004   0.040   1313
  Dihedral  :  7.606 121.836   1036
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.52 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  1.30 (0.28), residues: 903
  helix:  2.08 (0.25), residues: 441
  sheet: -0.72 (0.57), residues: 54
  loop : -0.24 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 150 
 TYR   0.012   0.001   TYR I  91 
 PHE   0.012   0.001   PHE I 110 
 TRP   0.005   0.001   TRP I  11 
 HIS   0.004   0.001   HIS K  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7652)
  covalent geometry    : angle       0.55467 (10370)
  hydrogen bonds       : bond        0.04411 (  362)
  hydrogen bonds       : angle       4.47072 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.251 
Fit side-chains
REVERT: H  265 MET cc_start: 0.8167 (mmm) cc_final: 0.7875 (mmm)
REVERT: I    8 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8734 (tttm)
REVERT: I   75 MET cc_start: 0.8249 (mtp) cc_final: 0.8031 (ttt)
REVERT: I  227 THR cc_start: 0.8293 (t) cc_final: 0.7666 (m)
REVERT: J  137 ASP cc_start: 0.9120 (t0) cc_final: 0.8907 (t70)
REVERT: K   85 GLN cc_start: 0.8462 (pt0) cc_final: 0.8194 (pt0)
REVERT: K  127 ASP cc_start: 0.8530 (t70) cc_final: 0.8275 (t70)
REVERT: K  223 ASP cc_start: 0.8199 (p0) cc_final: 0.7843 (p0)
  outliers start: 22
  outliers final: 3
  residues processed: 129
  average time/residue: 0.5993
  time to fit residues: 80.9666
Evaluate side-chains
  109 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LYS
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  147 GLU
Chi-restraints excluded: chain K residue   69 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 48 optimal weight:   10.0000
   chunk 35 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9980
   chunk 86 optimal weight:    8.9990
   chunk 71 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 77 optimal weight:    0.4980
   chunk 13 optimal weight:    6.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    1.7182

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
K 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.107664 restraints weight = 9474.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.98
r_work: 0.3218 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.0858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7652  Z= 0.148
  Angle     :  0.587   7.668  10370  Z= 0.283
  Chirality :  0.043   0.143   1146
  Planarity :  0.004   0.040   1313
  Dihedral  :  7.234 121.070   1026
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 19.65 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  1.25 (0.27), residues: 903
  helix:  2.06 (0.25), residues: 440
  sheet: -0.66 (0.58), residues: 56
  loop : -0.29 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 167 
 TYR   0.013   0.001   TYR I  91 
 PHE   0.015   0.001   PHE H 305 
 TRP   0.008   0.001   TRP I  11 
 HIS   0.004   0.001   HIS K  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 7652)
  covalent geometry    : angle       0.58658 (10370)
  hydrogen bonds       : bond        0.04739 (  362)
  hydrogen bonds       : angle       4.41701 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.269 
Fit side-chains
REVERT: H  265 MET cc_start: 0.8204 (mmm) cc_final: 0.7968 (mmm)
REVERT: I    8 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8752 (tttm)
REVERT: K   85 GLN cc_start: 0.8441 (pt0) cc_final: 0.8193 (pt0)
REVERT: K  223 ASP cc_start: 0.8214 (p0) cc_final: 0.7857 (p0)
REVERT: K  248 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7685 (m-10)
  outliers start: 30
  outliers final: 8
  residues processed: 124
  average time/residue: 0.5413
  time to fit residues: 70.5379
Evaluate side-chains
  111 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    8 LYS
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  147 GLU
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue  292 MET
Chi-restraints excluded: chain K residue   32 LEU
Chi-restraints excluded: chain K residue   69 VAL
Chi-restraints excluded: chain K residue  248 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 89 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 61 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
K 131 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.133661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.107270 restraints weight = 9655.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.00
r_work: 0.3213 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.0960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7652  Z= 0.151
  Angle     :  0.593   8.121  10370  Z= 0.284
  Chirality :  0.043   0.144   1146
  Planarity :  0.004   0.040   1313
  Dihedral  :  7.259 120.681   1026
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.40 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: 903
  helix:  2.07 (0.25), residues: 440
  sheet: -0.67 (0.58), residues: 58
  loop : -0.29 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 167 
 TYR   0.013   0.001   TYR I  91 
 PHE   0.014   0.002   PHE H 305 
 TRP   0.008   0.001   TRP I  11 
 HIS   0.004   0.001   HIS K  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7652)
  covalent geometry    : angle       0.59256 (10370)
  hydrogen bonds       : bond        0.04726 (  362)
  hydrogen bonds       : angle       4.35742 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.215 
Fit side-chains
REVERT: I    8 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8809 (tttm)
REVERT: I   61 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7946 (tp30)
REVERT: I  229 GLU cc_start: 0.8184 (pm20) cc_final: 0.7852 (pm20)
REVERT: K   85 GLN cc_start: 0.8438 (pt0) cc_final: 0.8172 (pt0)
REVERT: K  223 ASP cc_start: 0.8150 (p0) cc_final: 0.7824 (p0)
REVERT: K  248 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7683 (m-10)
  outliers start: 25
  outliers final: 9
  residues processed: 114
  average time/residue: 0.5597
  time to fit residues: 67.0398
Evaluate side-chains
  109 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  268 ARG
Chi-restraints excluded: chain I residue    8 LYS
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   34 THR
Chi-restraints excluded: chain K residue   32 LEU
Chi-restraints excluded: chain K residue   69 VAL
Chi-restraints excluded: chain K residue  124 LEU
Chi-restraints excluded: chain K residue  248 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0980
   chunk 18 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   chunk 75 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
K 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.131906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.105683 restraints weight = 9559.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.97
r_work: 0.3190 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   7652  Z= 0.210
  Angle     :  0.654   7.654  10370  Z= 0.316
  Chirality :  0.046   0.158   1146
  Planarity :  0.005   0.044   1313
  Dihedral  :  7.534 126.214   1026
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.40 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  1.01 (0.27), residues: 903
  helix:  1.83 (0.24), residues: 440
  sheet: -0.74 (0.58), residues: 58
  loop : -0.38 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J 167 
 TYR   0.014   0.002   TYR I  91 
 PHE   0.018   0.002   PHE H 305 
 TRP   0.011   0.002   TRP J 237 
 HIS   0.005   0.001   HIS J 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 7652)
  covalent geometry    : angle       0.65449 (10370)
  hydrogen bonds       : bond        0.05507 (  362)
  hydrogen bonds       : angle       4.48343 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.292 
Fit side-chains
REVERT: I   61 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8050 (tp30)
REVERT: I  278 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7780 (mm-30)
REVERT: K   85 GLN cc_start: 0.8459 (pt0) cc_final: 0.8196 (pt0)
REVERT: K  223 ASP cc_start: 0.8138 (p0) cc_final: 0.7860 (p0)
REVERT: K  248 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7783 (m-10)
REVERT: K  291 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6039 (ttmm)
  outliers start: 24
  outliers final: 10
  residues processed: 114
  average time/residue: 0.5984
  time to fit residues: 71.5920
Evaluate side-chains
  110 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  147 GLU
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain J residue   34 THR
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  292 MET
Chi-restraints excluded: chain K residue   32 LEU
Chi-restraints excluded: chain K residue   69 VAL
Chi-restraints excluded: chain K residue  124 LEU
Chi-restraints excluded: chain K residue  248 PHE
Chi-restraints excluded: chain K residue  291 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
H 273 ASN
K 131 GLN
K 268 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.109016 restraints weight = 9526.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.99
r_work: 0.3235 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7652  Z= 0.107
  Angle     :  0.560   7.851  10370  Z= 0.266
  Chirality :  0.041   0.132   1146
  Planarity :  0.004   0.042   1313
  Dihedral  :  7.144 118.029   1026
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.89 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  1.43 (0.28), residues: 903
  helix:  2.24 (0.25), residues: 440
  sheet: -0.62 (0.60), residues: 56
  loop : -0.24 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  22 
 TYR   0.014   0.001   TYR I  60 
 PHE   0.009   0.001   PHE I 110 
 TRP   0.007   0.001   TRP I  11 
 HIS   0.003   0.001   HIS K  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7652)
  covalent geometry    : angle       0.55950 (10370)
  hydrogen bonds       : bond        0.03991 (  362)
  hydrogen bonds       : angle       4.20465 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.203 
Fit side-chains
REVERT: I   61 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7903 (tp30)
REVERT: I  229 GLU cc_start: 0.8195 (pm20) cc_final: 0.7957 (pm20)
REVERT: I  278 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7867 (mm-30)
REVERT: K   85 GLN cc_start: 0.8301 (pt0) cc_final: 0.8061 (pt0)
REVERT: K  127 ASP cc_start: 0.8424 (t70) cc_final: 0.8159 (t70)
REVERT: K  223 ASP cc_start: 0.8162 (p0) cc_final: 0.7900 (p0)
REVERT: K  248 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7638 (m-10)
  outliers start: 17
  outliers final: 8
  residues processed: 115
  average time/residue: 0.5866
  time to fit residues: 70.6365
Evaluate side-chains
  115 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   61 GLU
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  147 GLU
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue  292 MET
Chi-restraints excluded: chain K residue   32 LEU
Chi-restraints excluded: chain K residue   69 VAL
Chi-restraints excluded: chain K residue  124 LEU
Chi-restraints excluded: chain K residue  248 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 84 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 51 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0370
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.9262

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
K 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.135422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.109255 restraints weight = 9462.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.98
r_work: 0.3241 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7652  Z= 0.113
  Angle     :  0.568   7.968  10370  Z= 0.270
  Chirality :  0.041   0.134   1146
  Planarity :  0.004   0.040   1313
  Dihedral  :  7.008 113.525   1026
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 20.77 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  1.56 (0.28), residues: 903
  helix:  2.35 (0.25), residues: 435
  sheet: -0.54 (0.59), residues: 56
  loop : -0.15 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K  22 
 TYR   0.013   0.001   TYR I  60 
 PHE   0.013   0.001   PHE I  71 
 TRP   0.007   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7652)
  covalent geometry    : angle       0.56838 (10370)
  hydrogen bonds       : bond        0.03989 (  362)
  hydrogen bonds       : angle       4.12730 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.248 
Fit side-chains
REVERT: H  247 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7471 (mp0)
REVERT: H  249 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7484 (pm20)
REVERT: I  229 GLU cc_start: 0.8198 (pm20) cc_final: 0.7968 (pm20)
REVERT: J   20 GLU cc_start: 0.8766 (tt0) cc_final: 0.8359 (tm-30)
REVERT: K   85 GLN cc_start: 0.8246 (pt0) cc_final: 0.8028 (pt0)
REVERT: K  127 ASP cc_start: 0.8442 (t70) cc_final: 0.8178 (t70)
REVERT: K  223 ASP cc_start: 0.8071 (p0) cc_final: 0.7829 (p0)
REVERT: K  248 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7628 (m-10)
  outliers start: 17
  outliers final: 8
  residues processed: 116
  average time/residue: 0.5814
  time to fit residues: 70.7902
Evaluate side-chains
  111 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  247 GLU
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  147 GLU
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue  292 MET
Chi-restraints excluded: chain K residue   32 LEU
Chi-restraints excluded: chain K residue   69 VAL
Chi-restraints excluded: chain K residue  124 LEU
Chi-restraints excluded: chain K residue  248 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 17 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 61 optimal weight:   20.0000
   chunk 79 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 132 ASN
K 161 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.130463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.104262 restraints weight = 9620.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.96
r_work: 0.3167 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.103   7652  Z= 0.307
  Angle     :  0.753  11.814  10370  Z= 0.366
  Chirality :  0.050   0.176   1146
  Planarity :  0.006   0.052   1313
  Dihedral  :  7.703 127.917   1026
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.01 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  0.77 (0.27), residues: 903
  helix:  1.55 (0.24), residues: 440
  sheet: -0.67 (0.58), residues: 58
  loop : -0.41 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  22 
 TYR   0.017   0.003   TYR K 168 
 PHE   0.022   0.003   PHE H 305 
 TRP   0.016   0.003   TRP J 237 
 HIS   0.006   0.002   HIS J 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00753 ( 7652)
  covalent geometry    : angle       0.75252 (10370)
  hydrogen bonds       : bond        0.06325 (  362)
  hydrogen bonds       : angle       4.61991 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.277 
Fit side-chains
REVERT: I   51 HIS cc_start: 0.7843 (p-80) cc_final: 0.7577 (p90)
REVERT: I   75 MET cc_start: 0.8546 (mtp) cc_final: 0.8202 (ttt)
REVERT: I   77 ARG cc_start: 0.7814 (ttp-170) cc_final: 0.7508 (ttp-170)
REVERT: I  229 GLU cc_start: 0.8245 (pm20) cc_final: 0.8000 (pm20)
REVERT: I  250 ASP cc_start: 0.7693 (m-30) cc_final: 0.7338 (m-30)
REVERT: K   85 GLN cc_start: 0.8442 (pt0) cc_final: 0.8204 (pt0)
REVERT: K  223 ASP cc_start: 0.8156 (p0) cc_final: 0.7925 (p0)
REVERT: K  248 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7810 (m-10)
REVERT: K  291 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6065 (ttmm)
  outliers start: 21
  outliers final: 10
  residues processed: 118
  average time/residue: 0.6290
  time to fit residues: 77.6462
Evaluate side-chains
  114 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  147 GLU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue   34 THR
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  292 MET
Chi-restraints excluded: chain K residue   32 LEU
Chi-restraints excluded: chain K residue   69 VAL
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue  124 LEU
Chi-restraints excluded: chain K residue  248 PHE
Chi-restraints excluded: chain K residue  291 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 9 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 23 optimal weight:    0.3980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
K 131 GLN
K 161 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.134795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.108629 restraints weight = 9498.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.97
r_work: 0.3230 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7652  Z= 0.115
  Angle     :  0.610  15.547  10370  Z= 0.288
  Chirality :  0.042   0.131   1146
  Planarity :  0.004   0.042   1313
  Dihedral  :  7.191 118.477   1026
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 22.13 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  1.28 (0.27), residues: 903
  helix:  2.10 (0.25), residues: 438
  sheet: -0.58 (0.59), residues: 56
  loop : -0.30 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  22 
 TYR   0.014   0.001   TYR I  60 
 PHE   0.013   0.001   PHE I  71 
 TRP   0.008   0.001   TRP I  11 
 HIS   0.005   0.001   HIS J  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7652)
  covalent geometry    : angle       0.61027 (10370)
  hydrogen bonds       : bond        0.04115 (  362)
  hydrogen bonds       : angle       4.27122 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.259 
Fit side-chains
REVERT: I  229 GLU cc_start: 0.8164 (pm20) cc_final: 0.7946 (pm20)
REVERT: I  248 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7636 (tt)
REVERT: J   20 GLU cc_start: 0.8748 (tt0) cc_final: 0.8336 (tm-30)
REVERT: K   85 GLN cc_start: 0.8256 (pt0) cc_final: 0.8027 (pt0)
REVERT: K  127 ASP cc_start: 0.8421 (t70) cc_final: 0.8176 (t70)
REVERT: K  223 ASP cc_start: 0.8096 (p0) cc_final: 0.7852 (p0)
REVERT: K  248 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7640 (m-10)
  outliers start: 12
  outliers final: 6
  residues processed: 118
  average time/residue: 0.6304
  time to fit residues: 77.6226
Evaluate side-chains
  111 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  147 GLU
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue  292 MET
Chi-restraints excluded: chain K residue   69 VAL
Chi-restraints excluded: chain K residue  124 LEU
Chi-restraints excluded: chain K residue  248 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 63 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** J  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 161 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.132424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.106306 restraints weight = 9522.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.97
r_work: 0.3197 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   7652  Z= 0.190
  Angle     :  0.681  16.321  10370  Z= 0.325
  Chirality :  0.045   0.154   1146
  Planarity :  0.005   0.041   1313
  Dihedral  :  7.362 121.409   1026
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 22.99 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  1.08 (0.27), residues: 903
  helix:  1.91 (0.25), residues: 438
  sheet: -0.66 (0.58), residues: 58
  loop : -0.37 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  22 
 TYR   0.014   0.002   TYR I  91 
 PHE   0.013   0.002   PHE I  71 
 TRP   0.009   0.002   TRP J 237 
 HIS   0.006   0.001   HIS J  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 7652)
  covalent geometry    : angle       0.68092 (10370)
  hydrogen bonds       : bond        0.05167 (  362)
  hydrogen bonds       : angle       4.44835 ( 1020)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.223 
Fit side-chains
REVERT: H  247 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7437 (mp0)
REVERT: I  229 GLU cc_start: 0.8225 (pm20) cc_final: 0.8011 (pm20)
REVERT: I  248 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7653 (tt)
REVERT: I  250 ASP cc_start: 0.7668 (m-30) cc_final: 0.7315 (m-30)
REVERT: J   20 GLU cc_start: 0.8767 (tt0) cc_final: 0.8337 (tm-30)
REVERT: K   85 GLN cc_start: 0.8366 (pt0) cc_final: 0.8125 (pt0)
REVERT: K  223 ASP cc_start: 0.8114 (p0) cc_final: 0.7876 (p0)
REVERT: K  248 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7755 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 109
  average time/residue: 0.5642
  time to fit residues: 64.3357
Evaluate side-chains
  112 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  247 GLU
Chi-restraints excluded: chain I residue  126 VAL
Chi-restraints excluded: chain I residue  147 GLU
Chi-restraints excluded: chain I residue  248 LEU
Chi-restraints excluded: chain I residue  270 VAL
Chi-restraints excluded: chain J residue  292 MET
Chi-restraints excluded: chain K residue   69 VAL
Chi-restraints excluded: chain K residue  124 LEU
Chi-restraints excluded: chain K residue  248 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
K 121 HIS
** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 161 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.135689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.109753 restraints weight = 9474.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.96
r_work: 0.3245 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7652  Z= 0.115
  Angle     :  0.614  16.721  10370  Z= 0.289
  Chirality :  0.042   0.139   1146
  Planarity :  0.004   0.041   1313
  Dihedral  :  7.007 112.228   1026
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 22.99 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  1.37 (0.28), residues: 903
  helix:  2.18 (0.25), residues: 439
  sheet: -0.54 (0.56), residues: 66
  loop : -0.25 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG J 309 
 TYR   0.014   0.001   TYR I  60 
 PHE   0.013   0.001   PHE I  71 
 TRP   0.007   0.001   TRP I  11 
 HIS   0.006   0.001   HIS J  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7652)
  covalent geometry    : angle       0.61361 (10370)
  hydrogen bonds       : bond        0.03941 (  362)
  hydrogen bonds       : angle       4.24555 ( 1020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2657.43 seconds
wall clock time: 45 minutes 51.99 seconds (2751.99 seconds total)