Starting phenix.real_space_refine
on Tue Feb  3 22:02:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i9i_52758/02_2026/9i9i_52758.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i9i_52758/02_2026/9i9i_52758.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i9i_52758/02_2026/9i9i_52758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i9i_52758/02_2026/9i9i_52758.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i9i_52758/02_2026/9i9i_52758.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i9i_52758/02_2026/9i9i_52758.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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       5      5.49       5
     Mg      2      5.21       5
     S      41      5.16       5
     C    4727      2.51       5
     N    1246      2.21       5
     O    1323      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  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: 7344
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "K"
      Number of atoms: 2186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2186
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 17, 'TRANS': 250}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    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: 2247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2247
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 275, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 260}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2342
          Classifications: {'peptide': 294}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 275}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "J"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2, 'water': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 1.41, per 1000 atoms: 0.19
  Number of scatterers: 7344
  At special positions: 0
  Unit cell: (81.6, 99.96, 111.18, 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      41     16.00
     P       5     15.00
     Mg      2     11.99
     O    1323      8.00
     N    1246      7.00
     C    4727      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: 0.67
  Conformation dependent library (CDL) restraints added in 189.6 milliseconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 6 sheets defined
      56.5% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'K' and resid 483 through 492
      removed outlier: 3.502A  pdb=" N   ALA K 492 " --> pdb=" O   THR K 488 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 523 through 529
    Processing helix  chain 'K' and resid 535 through 556
    Processing helix  chain 'K' and resid 580 through 584
      removed outlier: 4.218A  pdb=" N   LEU K 583 " --> pdb=" O   ASP K 580 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 605 through 610
    Processing helix  chain 'K' and resid 617 through 634
    Processing helix  chain 'K' and resid 642 through 655
    Processing helix  chain 'K' and resid 668 through 674
    Processing helix  chain 'K' and resid 693 through 704
    Processing helix  chain 'K' and resid 713 through 719
    Processing helix  chain 'K' and resid 720 through 724
      removed outlier: 3.568A  pdb=" N   PHE K 723 " --> pdb=" O   HIS K 720 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 262 through 275
      removed outlier: 3.644A  pdb=" N   LEU H 266 " --> pdb=" O   LEU H 263 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLY H 267 " --> pdb=" O   GLU H 264 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   TYR H 271 " --> pdb=" O   ARG H 268 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LEU H 272 " --> pdb=" O   LEU H 269 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 279 through 285
      removed outlier: 3.519A  pdb=" N   GLY H 285 " --> pdb=" O   GLN H 281 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 288 through 301
      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: 3.786A  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: 3.826A  pdb=" N   LEU I  19 " --> pdb=" O   SER I  15 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 49 through 70
      removed outlier: 3.554A  pdb=" N   VAL I  70 " --> pdb=" O   GLU I  66 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 76 through 94
      removed outlier: 3.949A  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 127
    Processing helix  chain 'I' and resid 132 through 154
      removed outlier: 4.689A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.477A  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
      removed outlier: 3.671A  pdb=" N   ILE I 186 " --> pdb=" O   ASN I 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 183 through 186'
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.707A  pdb=" N   ALA I 191 " --> pdb=" O   LEU I 187 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 224
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.828A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 243 through 262
    Processing helix  chain 'I' and resid 266 through 284
    Processing helix  chain 'J' and resid 47 through 52
      removed outlier: 3.872A  pdb=" N   LYS J  52 " --> pdb=" O   ARG J  48 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 56 through 68
    Processing helix  chain 'J' and resid 98 through 104
    Processing helix  chain 'J' and resid 110 through 131
      removed outlier: 3.592A  pdb=" N   HIS J 131 " --> pdb=" O   TYR J 127 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 139 through 142
    Processing helix  chain 'J' and resid 175 through 179
      removed outlier: 3.786A  pdb=" N   ARG J 179 " --> pdb=" O   ARG J 176 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 180 through 185
    Processing helix  chain 'J' and resid 192 through 209
      removed outlier: 4.080A  pdb=" N   ALA J 198 " --> pdb=" O   VAL J 194 " (cutoff:3.500A)
    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
      removed outlier: 3.534A  pdb=" N   ILE J 260 " --> pdb=" O   PRO J 256 " (cutoff:3.500A)
    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: 4.230A  pdb=" N   SER J 296 " --> pdb=" O   MET J 292 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 303 through 307
      removed outlier: 3.698A  pdb=" N   LEU J 307 " --> pdb=" O   GLY J 304 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 442 through 445
      removed outlier: 3.554A  pdb=" N   ASN K 442 " --> pdb=" O   ARG K 454 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   VAL K 452 " --> pdb=" O   ILE K 444 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ILE K 512 " --> pdb=" O   LEU K 469 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   TYR K 513 " --> pdb=" O   ILE K 503 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   ILE K 503 " --> pdb=" O   TYR K 513 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   VAL K 515 " --> pdb=" O   ARG K 501 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 521 through 522
    Processing sheet with id=AA3, first strand: chain 'K' and resid 558 through 559
    Processing sheet with id=AA4, first strand: chain 'J' and resid 14 through 20
      removed outlier: 4.380A  pdb=" N   ASP J  16 " --> pdb=" O   LYS J  28 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   VAL J  26 " --> pdb=" O   LEU J  18 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   GLU J  20 " --> pdb=" O   ALA J  24 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ALA J  24 " --> pdb=" O   GLU J  20 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL J  90 " --> pdb=" O   LEU J  78 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 96 through 97
    Processing sheet with id=AA6, first strand: chain 'J' and resid 133 through 134

    348 hydrogen bonds defined for protein.
    978 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: 0.74

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2324
        1.34 -     1.46: 1364
        1.46 -     1.58: 3758
        1.58 -     1.69: 6
        1.69 -     1.81: 68
  Bond restraints: 7520
  Sorted by residual:
  bond pdb=" C   ACE I   0 "
       pdb=" O   ACE I   0 "
    ideal  model  delta    sigma   weight residual
    1.199  1.229 -0.030 2.00e-02 2.50e+03 2.29e+00
  bond pdb=" CB  LYS I 260 "
       pdb=" CG  LYS I 260 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.31e+00
  bond pdb=" CB  ASP K 731 "
       pdb=" CG  ASP K 731 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.11e+00
  bond pdb=" C4  ADP J 401 "
       pdb=" C5  ADP J 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.469  0.021 2.00e-02 2.50e+03 1.11e+00
  bond pdb=" C4  ADP K 801 "
       pdb=" C5  ADP K 801 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 9.63e-01
  ... (remaining 7515 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 9822
        1.25 -     2.50: 244
        2.50 -     3.76: 83
        3.76 -     5.01: 23
        5.01 -     6.26: 16
  Bond angle restraints: 10188
  Sorted by residual:
  angle pdb=" CA  GLN K 634 "
        pdb=" CB  GLN K 634 "
        pdb=" CG  GLN K 634 "
      ideal   model   delta    sigma   weight residual
     114.10  120.02   -5.92 2.00e+00 2.50e-01 8.77e+00
  angle pdb=" CA  LYS I 260 "
        pdb=" CB  LYS I 260 "
        pdb=" CG  LYS I 260 "
      ideal   model   delta    sigma   weight residual
     114.10  119.85   -5.75 2.00e+00 2.50e-01 8.28e+00
  angle pdb=" CB  LYS I 260 "
        pdb=" CG  LYS I 260 "
        pdb=" CD  LYS I 260 "
      ideal   model   delta    sigma   weight residual
     111.30  116.98   -5.68 2.30e+00 1.89e-01 6.10e+00
  angle pdb=" CA  GLN I 124 "
        pdb=" CB  GLN I 124 "
        pdb=" CG  GLN I 124 "
      ideal   model   delta    sigma   weight residual
     114.10  118.87   -4.77 2.00e+00 2.50e-01 5.69e+00
  angle pdb=" C   ASP K 731 "
        pdb=" CA  ASP K 731 "
        pdb=" CB  ASP K 731 "
      ideal   model   delta    sigma   weight residual
     109.27  112.94   -3.67 1.61e+00 3.86e-01 5.21e+00
  ... (remaining 10183 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3886
       17.96 -    35.91: 479
       35.91 -    53.87: 123
       53.87 -    71.82: 19
       71.82 -    89.78: 16
  Dihedral angle restraints: 4523
    sinusoidal: 1888
      harmonic: 2635
  Sorted by residual:
  dihedral pdb=" CA  MET J  94 "
           pdb=" C   MET J  94 "
           pdb=" N   GLU J  95 "
           pdb=" CA  GLU J  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.29  -16.71     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CG  ARG K 501 "
           pdb=" CD  ARG K 501 "
           pdb=" NE  ARG K 501 "
           pdb=" CZ  ARG K 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  135.00  -45.00     2      1.50e+01 4.44e-03 1.07e+01
  dihedral pdb=" CB  GLU H 264 "
           pdb=" CG  GLU H 264 "
           pdb=" CD  GLU H 264 "
           pdb=" OE1 GLU H 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.40   88.40     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 4520 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 667
       0.026 -    0.053: 262
       0.053 -    0.079: 109
       0.079 -    0.105: 64
       0.105 -    0.132: 22
  Chirality restraints: 1124
  Sorted by residual:
  chirality pdb=" CA  ILE J  87 "
            pdb=" N   ILE J  87 "
            pdb=" C   ILE J  87 "
            pdb=" CB  ILE J  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE K 497 "
            pdb=" N   ILE K 497 "
            pdb=" C   ILE K 497 "
            pdb=" CB  ILE K 497 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  THR K 726 "
            pdb=" N   THR K 726 "
            pdb=" C   THR K 726 "
            pdb=" CB  THR K 726 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.09e-01
  ... (remaining 1121 not shown)

  Planarity restraints: 1283
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN K 532 "    0.035 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO K 533 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO K 533 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO K 533 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU I 141 "   -0.007 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" CD  GLU I 141 "    0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU I 141 "   -0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU I 141 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 246 "   -0.006 2.00e-02 2.50e+03   9.48e-03 1.80e+00
        pdb=" CG  TYR H 246 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 246 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 246 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 246 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 246 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 246 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR H 246 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1280 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 44
        2.53 -     3.12: 5481
        3.12 -     3.71: 11613
        3.71 -     4.31: 15894
        4.31 -     4.90: 26681
  Nonbonded interactions: 59713
  Sorted by model distance:
  nonbonded pdb=" O2A ADP K 801 "
            pdb="MG    MG K 802 "
     model   vdw
     1.935 2.170
  nonbonded pdb=" OD2 ASP K 580 "
            pdb="MG    MG K 802 "
     model   vdw
     2.031 2.170
  nonbonded pdb=" N   GLU I 229 "
            pdb=" OE1 GLU I 229 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OG1 THR K 541 "
            pdb=" O   ILE K 730 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NZ  LYS J 139 "
            pdb=" OD1 ASN J 141 "
     model   vdw
     2.235 3.120
  ... (remaining 59708 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.770
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7520  Z= 0.123
  Angle     :  0.599   6.260  10188  Z= 0.297
  Chirality :  0.040   0.132   1124
  Planarity :  0.004   0.054   1283
  Dihedral  : 17.242  89.776   2817
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.48 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 21.23 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.14 (0.29), residues: 876
  helix:  1.87 (0.25), residues: 443
  sheet: -1.08 (0.76), residues: 49
  loop : -0.27 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J 298 
 TYR   0.023   0.001   TYR H 246 
 PHE   0.022   0.001   PHE K 703 
 TRP   0.007   0.001   TRP K 557 
 HIS   0.004   0.001   HIS H 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7520)
  covalent geometry    : angle       0.59918 (10188)
  hydrogen bonds       : bond        0.15749 (  348)
  hydrogen bonds       : angle       5.78927 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  515 VAL cc_start: 0.7259 (t) cc_final: 0.6931 (p)
REVERT: K  534 PHE cc_start: 0.6043 (OUTLIER) cc_final: 0.4644 (t80)
REVERT: J  137 ASP cc_start: 0.8213 (t0) cc_final: 0.7705 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 155
  average time/residue: 0.0640
  time to fit residues: 14.0323
Evaluate side-chains
  145 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  463 ILE
Chi-restraints excluded: chain K residue  523 LEU
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  728 LEU
Chi-restraints excluded: chain I residue   32 CYS
Chi-restraints excluded: chain I residue   35 VAL
Chi-restraints excluded: chain I residue  128 ASN
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  202 ASP
Chi-restraints excluded: chain I residue  222 SER
Chi-restraints excluded: chain J residue   96 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
K 556 ASN
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.140450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.108818 restraints weight = 12412.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.111895 restraints weight = 6524.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.113813 restraints weight = 4393.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.115048 restraints weight = 3437.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.115747 restraints weight = 2937.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7520  Z= 0.191
  Angle     :  0.615   9.052  10188  Z= 0.302
  Chirality :  0.042   0.144   1124
  Planarity :  0.004   0.036   1283
  Dihedral  :  6.568  59.099   1022
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.94 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.72 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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 (0.29), residues: 876
  helix:  2.08 (0.25), residues: 441
  sheet: -0.99 (0.84), residues: 39
  loop : -0.35 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  31 
 TYR   0.014   0.002   TYR H 271 
 PHE   0.019   0.001   PHE K 703 
 TRP   0.007   0.001   TRP K 662 
 HIS   0.005   0.001   HIS J 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 7520)
  covalent geometry    : angle       0.61535 (10188)
  hydrogen bonds       : bond        0.04722 (  348)
  hydrogen bonds       : angle       4.68831 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  527 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7316 (mmm)
REVERT: K  530 MET cc_start: 0.6593 (tmm) cc_final: 0.6340 (tmm)
REVERT: K  534 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.4970 (t80)
REVERT: K  705 THR cc_start: 0.5066 (OUTLIER) cc_final: 0.4860 (p)
REVERT: I  124 GLN cc_start: 0.8275 (tp40) cc_final: 0.7868 (tp40)
REVERT: I  136 GLN cc_start: 0.7068 (mt0) cc_final: 0.6539 (mp10)
REVERT: I  266 ARG cc_start: 0.6478 (mtt90) cc_final: 0.5651 (mmm160)
REVERT: J  137 ASP cc_start: 0.8385 (t0) cc_final: 0.7924 (t0)
  outliers start: 25
  outliers final: 11
  residues processed: 155
  average time/residue: 0.0680
  time to fit residues: 14.9101
Evaluate side-chains
  143 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  522 ASP
Chi-restraints excluded: chain K residue  527 MET
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  608 LEU
Chi-restraints excluded: chain K residue  617 THR
Chi-restraints excluded: chain K residue  643 GLU
Chi-restraints excluded: chain K residue  700 MET
Chi-restraints excluded: chain K residue  705 THR
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  176 THR
Chi-restraints excluded: chain J residue   66 LEU
Chi-restraints excluded: chain J residue  182 GLU
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  242 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 39 optimal weight:    0.4980
   chunk 17 optimal weight:    0.6980
   chunk 23 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
K 556 ASN
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.143079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.111956 restraints weight = 12434.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.114986 restraints weight = 6729.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.116867 restraints weight = 4550.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.118062 restraints weight = 3562.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.118736 restraints weight = 3045.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7520  Z= 0.135
  Angle     :  0.570   6.910  10188  Z= 0.276
  Chirality :  0.041   0.141   1124
  Planarity :  0.004   0.031   1283
  Dihedral  :  5.996  57.421   1008
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.94 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 20.98 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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 (0.29), residues: 876
  helix:  2.14 (0.25), residues: 441
  sheet: -0.85 (0.75), residues: 46
  loop : -0.35 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  31 
 TYR   0.016   0.001   TYR H 246 
 PHE   0.014   0.001   PHE K 703 
 TRP   0.005   0.001   TRP J 197 
 HIS   0.003   0.001   HIS J 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7520)
  covalent geometry    : angle       0.56966 (10188)
  hydrogen bonds       : bond        0.04023 (  348)
  hydrogen bonds       : angle       4.44674 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  704 LEU cc_start: 0.6165 (pp) cc_final: 0.5909 (pp)
REVERT: I  124 GLN cc_start: 0.8188 (tp40) cc_final: 0.7864 (tt0)
REVERT: I  140 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7675 (mt)
REVERT: J  137 ASP cc_start: 0.8327 (t0) cc_final: 0.7866 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 159
  average time/residue: 0.0679
  time to fit residues: 15.0073
Evaluate side-chains
  146 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  522 ASP
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  608 LEU
Chi-restraints excluded: chain K residue  619 VAL
Chi-restraints excluded: chain I residue  140 LEU
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain J residue   66 LEU
Chi-restraints excluded: chain J residue  182 GLU
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  242 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0170
   chunk 27 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 2 optimal weight:    8.9990
   chunk 62 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.2026

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

Flipped N/Q/H residues before XYZ refinement:
K 556 ASN
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I   3 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.143873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.112573 restraints weight = 12550.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.115604 restraints weight = 6758.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.117540 restraints weight = 4580.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.118675 restraints weight = 3573.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.119491 restraints weight = 3067.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7520  Z= 0.120
  Angle     :  0.569   8.901  10188  Z= 0.275
  Chirality :  0.040   0.129   1124
  Planarity :  0.004   0.032   1283
  Dihedral  :  5.875  56.157   1008
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.83 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 21.86 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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 (0.29), residues: 876
  helix:  2.18 (0.25), residues: 441
  sheet: -0.95 (0.70), residues: 56
  loop : -0.36 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 685 
 TYR   0.014   0.001   TYR I  60 
 PHE   0.038   0.001   PHE K 703 
 TRP   0.005   0.001   TRP K 622 
 HIS   0.003   0.001   HIS H 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7520)
  covalent geometry    : angle       0.56885 (10188)
  hydrogen bonds       : bond        0.03744 (  348)
  hydrogen bonds       : angle       4.35996 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  546 LEU cc_start: 0.7527 (tp) cc_final: 0.7299 (pp)
REVERT: K  704 LEU cc_start: 0.6055 (pp) cc_final: 0.5854 (pp)
REVERT: I  124 GLN cc_start: 0.8194 (tp40) cc_final: 0.7894 (tt0)
REVERT: I  140 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7688 (mt)
REVERT: I  255 MET cc_start: 0.8250 (tpp) cc_final: 0.7993 (tpp)
REVERT: J  137 ASP cc_start: 0.8312 (t0) cc_final: 0.7819 (t0)
  outliers start: 18
  outliers final: 10
  residues processed: 155
  average time/residue: 0.0784
  time to fit residues: 16.9032
Evaluate side-chains
  145 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  463 ILE
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  608 LEU
Chi-restraints excluded: chain K residue  619 VAL
Chi-restraints excluded: chain K residue  624 VAL
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue  140 LEU
Chi-restraints excluded: chain J residue  182 GLU
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  213 LEU
Chi-restraints excluded: chain J residue  216 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 49 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0970
   chunk 59 optimal weight:    9.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
K 556 ASN
** K 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 281 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.145888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.114893 restraints weight = 12393.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.117952 restraints weight = 6655.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.119912 restraints weight = 4481.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.121180 restraints weight = 3474.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121982 restraints weight = 2939.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7520  Z= 0.102
  Angle     :  0.551   6.944  10188  Z= 0.264
  Chirality :  0.039   0.132   1124
  Planarity :  0.004   0.033   1283
  Dihedral  :  5.476  52.622   1006
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.94 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 22.86 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.48 (0.29), residues: 876
  helix:  2.22 (0.25), residues: 447
  sheet: -0.71 (0.85), residues: 39
  loop : -0.29 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 685 
 TYR   0.014   0.001   TYR I  60 
 PHE   0.030   0.001   PHE K 703 
 TRP   0.006   0.001   TRP J 197 
 HIS   0.008   0.001   HIS K 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7520)
  covalent geometry    : angle       0.55139 (10188)
  hydrogen bonds       : bond        0.03377 (  348)
  hydrogen bonds       : angle       4.24227 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  124 GLN cc_start: 0.8151 (tp40) cc_final: 0.7890 (tt0)
REVERT: I  140 LEU cc_start: 0.7874 (mt) cc_final: 0.7639 (mt)
REVERT: I  255 MET cc_start: 0.8189 (tpp) cc_final: 0.7967 (tpp)
REVERT: J   40 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6832 (mp)
REVERT: J  137 ASP cc_start: 0.8315 (t0) cc_final: 0.7818 (t0)
  outliers start: 18
  outliers final: 9
  residues processed: 159
  average time/residue: 0.0697
  time to fit residues: 15.3761
Evaluate side-chains
  147 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  463 ILE
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  608 LEU
Chi-restraints excluded: chain K residue  619 VAL
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  222 SER
Chi-restraints excluded: chain J residue   40 ILE
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  216 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 68 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 70 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
K 493 GLN
K 556 ASN
** K 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.144830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.113749 restraints weight = 12306.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.116760 restraints weight = 6671.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.118657 restraints weight = 4511.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.119881 restraints weight = 3514.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.120590 restraints weight = 2995.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7520  Z= 0.116
  Angle     :  0.567   8.515  10188  Z= 0.270
  Chirality :  0.040   0.134   1124
  Planarity :  0.004   0.030   1283
  Dihedral  :  5.417  52.891   1006
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.83 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 22.24 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.46 (0.29), residues: 876
  helix:  2.19 (0.25), residues: 448
  sheet: -0.83 (0.75), residues: 48
  loop : -0.25 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 685 
 TYR   0.013   0.001   TYR I  60 
 PHE   0.027   0.001   PHE K 703 
 TRP   0.005   0.001   TRP K 622 
 HIS   0.005   0.001   HIS K 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7520)
  covalent geometry    : angle       0.56694 (10188)
  hydrogen bonds       : bond        0.03479 (  348)
  hydrogen bonds       : angle       4.21751 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  485 GLU cc_start: 0.5358 (tt0) cc_final: 0.4971 (mp0)
REVERT: I  124 GLN cc_start: 0.8152 (tp40) cc_final: 0.7865 (tt0)
REVERT: I  140 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7536 (mt)
REVERT: I  255 MET cc_start: 0.8243 (tpp) cc_final: 0.8029 (tpp)
REVERT: J  137 ASP cc_start: 0.8275 (t0) cc_final: 0.7782 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 154
  average time/residue: 0.0763
  time to fit residues: 16.1597
Evaluate side-chains
  154 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  463 ILE
Chi-restraints excluded: chain K residue  494 HIS
Chi-restraints excluded: chain K residue  522 ASP
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  572 HIS
Chi-restraints excluded: chain K residue  608 LEU
Chi-restraints excluded: chain K residue  619 VAL
Chi-restraints excluded: chain K residue  643 GLU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  140 LEU
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  222 SER
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  216 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
K 556 ASN
** K 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.142962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.111738 restraints weight = 12471.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.114667 restraints weight = 6731.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.116536 restraints weight = 4577.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.117699 restraints weight = 3580.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.118452 restraints weight = 3066.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7520  Z= 0.148
  Angle     :  0.592   7.987  10188  Z= 0.284
  Chirality :  0.041   0.138   1124
  Planarity :  0.004   0.034   1283
  Dihedral  :  5.481  53.228   1006
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.83 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 21.73 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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 (0.29), residues: 876
  helix:  2.20 (0.25), residues: 442
  sheet: -1.02 (0.68), residues: 55
  loop : -0.31 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I  31 
 TYR   0.012   0.001   TYR I  91 
 PHE   0.025   0.001   PHE K 703 
 TRP   0.009   0.001   TRP K 622 
 HIS   0.006   0.001   HIS K 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7520)
  covalent geometry    : angle       0.59243 (10188)
  hydrogen bonds       : bond        0.03878 (  348)
  hydrogen bonds       : angle       4.26658 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  485 GLU cc_start: 0.5425 (tt0) cc_final: 0.5205 (mt-10)
REVERT: K  532 GLN cc_start: 0.7476 (mp10) cc_final: 0.6882 (pm20)
REVERT: K  546 LEU cc_start: 0.7559 (tp) cc_final: 0.7308 (pp)
REVERT: I  124 GLN cc_start: 0.8214 (tp40) cc_final: 0.7869 (tt0)
REVERT: I  140 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7693 (mt)
REVERT: I  255 MET cc_start: 0.8276 (tpp) cc_final: 0.8063 (tpp)
REVERT: J   40 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6839 (mp)
REVERT: J  130 GLN cc_start: 0.8151 (mt0) cc_final: 0.7843 (mt0)
REVERT: J  137 ASP cc_start: 0.8329 (t0) cc_final: 0.7863 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 154
  average time/residue: 0.0608
  time to fit residues: 13.0012
Evaluate side-chains
  154 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  463 ILE
Chi-restraints excluded: chain K residue  522 ASP
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  572 HIS
Chi-restraints excluded: chain K residue  576 LEU
Chi-restraints excluded: chain K residue  578 VAL
Chi-restraints excluded: chain K residue  608 LEU
Chi-restraints excluded: chain K residue  619 VAL
Chi-restraints excluded: chain K residue  624 VAL
Chi-restraints excluded: chain K residue  643 GLU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  140 LEU
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain J residue   40 ILE
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  216 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
K 556 ASN
** K 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.143580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.112236 restraints weight = 12519.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.115242 restraints weight = 6740.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.117141 restraints weight = 4551.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.118302 restraints weight = 3553.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.119015 restraints weight = 3043.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7520  Z= 0.129
  Angle     :  0.593   8.179  10188  Z= 0.283
  Chirality :  0.040   0.136   1124
  Planarity :  0.004   0.034   1283
  Dihedral  :  5.424  52.716   1006
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.83 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.73 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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 (0.29), residues: 876
  helix:  2.22 (0.25), residues: 441
  sheet: -1.02 (0.67), residues: 55
  loop : -0.33 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K 685 
 TYR   0.013   0.001   TYR I  60 
 PHE   0.024   0.001   PHE K 703 
 TRP   0.006   0.001   TRP K 622 
 HIS   0.008   0.001   HIS K 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7520)
  covalent geometry    : angle       0.59282 (10188)
  hydrogen bonds       : bond        0.03629 (  348)
  hydrogen bonds       : angle       4.19273 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  485 GLU cc_start: 0.5423 (tt0) cc_final: 0.5220 (mt-10)
REVERT: K  532 GLN cc_start: 0.7649 (mp10) cc_final: 0.6963 (pm20)
REVERT: K  546 LEU cc_start: 0.7540 (tp) cc_final: 0.7312 (pp)
REVERT: K  617 THR cc_start: 0.7935 (p) cc_final: 0.7673 (p)
REVERT: I  124 GLN cc_start: 0.8206 (tp40) cc_final: 0.7847 (tt0)
REVERT: I  140 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7652 (mt)
REVERT: I  255 MET cc_start: 0.8266 (tpp) cc_final: 0.8061 (tpp)
REVERT: J   40 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6873 (mp)
REVERT: J  130 GLN cc_start: 0.8168 (mt0) cc_final: 0.7855 (mt0)
REVERT: J  137 ASP cc_start: 0.8266 (t0) cc_final: 0.7803 (t0)
  outliers start: 24
  outliers final: 17
  residues processed: 148
  average time/residue: 0.0609
  time to fit residues: 12.6336
Evaluate side-chains
  154 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  463 ILE
Chi-restraints excluded: chain K residue  522 ASP
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  572 HIS
Chi-restraints excluded: chain K residue  578 VAL
Chi-restraints excluded: chain K residue  608 LEU
Chi-restraints excluded: chain K residue  619 VAL
Chi-restraints excluded: chain K residue  624 VAL
Chi-restraints excluded: chain K residue  643 GLU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  140 LEU
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  222 SER
Chi-restraints excluded: chain J residue   40 ILE
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  242 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 86 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   chunk 73 optimal weight:    0.0470
   chunk 66 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.9684

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

Flipped N/Q/H residues before XYZ refinement:
K 556 ASN
** K 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.142668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.111697 restraints weight = 12421.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.114611 restraints weight = 6731.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.116473 restraints weight = 4567.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.117654 restraints weight = 3567.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.118371 restraints weight = 3050.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7520  Z= 0.152
  Angle     :  0.608   7.628  10188  Z= 0.292
  Chirality :  0.041   0.137   1124
  Planarity :  0.004   0.035   1283
  Dihedral  :  5.456  52.627   1006
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.05 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.61 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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 (0.29), residues: 876
  helix:  2.16 (0.25), residues: 441
  sheet: -1.10 (0.67), residues: 55
  loop : -0.36 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  77 
 TYR   0.012   0.001   TYR H 271 
 PHE   0.024   0.001   PHE K 703 
 TRP   0.007   0.001   TRP K 622 
 HIS   0.007   0.001   HIS K 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 7520)
  covalent geometry    : angle       0.60765 (10188)
  hydrogen bonds       : bond        0.03823 (  348)
  hydrogen bonds       : angle       4.22994 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  485 GLU cc_start: 0.5414 (tt0) cc_final: 0.5194 (mt-10)
REVERT: K  532 GLN cc_start: 0.7781 (mp10) cc_final: 0.7112 (pm20)
REVERT: K  546 LEU cc_start: 0.7551 (tp) cc_final: 0.7325 (pp)
REVERT: K  617 THR cc_start: 0.7782 (p) cc_final: 0.7538 (p)
REVERT: I  124 GLN cc_start: 0.8241 (tp40) cc_final: 0.7972 (tp-100)
REVERT: I  140 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7702 (mt)
REVERT: J   20 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6930 (tm-30)
REVERT: J   40 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6857 (mp)
REVERT: J  130 GLN cc_start: 0.8231 (mt0) cc_final: 0.7938 (mt0)
REVERT: J  137 ASP cc_start: 0.8322 (t0) cc_final: 0.7827 (t0)
  outliers start: 25
  outliers final: 18
  residues processed: 149
  average time/residue: 0.0766
  time to fit residues: 15.8042
Evaluate side-chains
  156 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  463 ILE
Chi-restraints excluded: chain K residue  522 ASP
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  572 HIS
Chi-restraints excluded: chain K residue  576 LEU
Chi-restraints excluded: chain K residue  578 VAL
Chi-restraints excluded: chain K residue  608 LEU
Chi-restraints excluded: chain K residue  619 VAL
Chi-restraints excluded: chain K residue  624 VAL
Chi-restraints excluded: chain K residue  643 GLU
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  140 LEU
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  222 SER
Chi-restraints excluded: chain J residue   40 ILE
Chi-restraints excluded: chain J residue  182 GLU
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  242 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 80 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
K 556 ASN
** K 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.144609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.113798 restraints weight = 12424.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.116782 restraints weight = 6666.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.118688 restraints weight = 4483.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.119861 restraints weight = 3482.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.120599 restraints weight = 2974.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7520  Z= 0.115
  Angle     :  0.595   7.552  10188  Z= 0.284
  Chirality :  0.040   0.134   1124
  Planarity :  0.004   0.035   1283
  Dihedral  :  5.342  51.528   1006
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.83 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 22.49 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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 (0.29), residues: 876
  helix:  2.07 (0.25), residues: 448
  sheet: -0.94 (0.68), residues: 55
  loop : -0.36 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 685 
 TYR   0.014   0.001   TYR I  60 
 PHE   0.022   0.001   PHE I  67 
 TRP   0.007   0.001   TRP K 622 
 HIS   0.008   0.001   HIS K 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7520)
  covalent geometry    : angle       0.59495 (10188)
  hydrogen bonds       : bond        0.03374 (  348)
  hydrogen bonds       : angle       4.15716 (  978)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  532 GLN cc_start: 0.7697 (mp10) cc_final: 0.7059 (pm20)
REVERT: K  546 LEU cc_start: 0.7511 (tp) cc_final: 0.7307 (pp)
REVERT: K  586 GLU cc_start: 0.4664 (tp30) cc_final: 0.4321 (tp30)
REVERT: K  617 THR cc_start: 0.7546 (p) cc_final: 0.6914 (p)
REVERT: I  124 GLN cc_start: 0.8183 (tp40) cc_final: 0.7828 (tt0)
REVERT: I  140 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7567 (mt)
REVERT: I  255 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7920 (mpp)
REVERT: J   40 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6865 (mp)
REVERT: J  130 GLN cc_start: 0.8158 (mt0) cc_final: 0.7868 (mt0)
REVERT: J  137 ASP cc_start: 0.8265 (t0) cc_final: 0.7813 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 152
  average time/residue: 0.0749
  time to fit residues: 15.6300
Evaluate side-chains
  151 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  463 ILE
Chi-restraints excluded: chain K residue  534 PHE
Chi-restraints excluded: chain K residue  572 HIS
Chi-restraints excluded: chain K residue  576 LEU
Chi-restraints excluded: chain K residue  578 VAL
Chi-restraints excluded: chain K residue  608 LEU
Chi-restraints excluded: chain K residue  619 VAL
Chi-restraints excluded: chain I residue   96 VAL
Chi-restraints excluded: chain I residue  140 LEU
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  222 SER
Chi-restraints excluded: chain I residue  255 MET
Chi-restraints excluded: chain J residue   40 ILE
Chi-restraints excluded: chain J residue  194 VAL
Chi-restraints excluded: chain J residue  216 ASP
Chi-restraints excluded: chain J residue  242 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
K 556 ASN
** K 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.144230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.112782 restraints weight = 12439.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.115745 restraints weight = 6762.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.117640 restraints weight = 4603.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.118862 restraints weight = 3600.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.119496 restraints weight = 3071.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7520  Z= 0.130
  Angle     :  0.622  10.396  10188  Z= 0.295
  Chirality :  0.041   0.163   1124
  Planarity :  0.004   0.034   1283
  Dihedral  :  5.325  51.427   1006
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.83 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 22.49 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    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:  1.24 (0.29), residues: 876
  helix:  2.02 (0.25), residues: 448
  sheet: -0.96 (0.74), residues: 48
  loop : -0.37 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  31 
 TYR   0.013   0.001   TYR I  60 
 PHE   0.024   0.001   PHE K 703 
 TRP   0.004   0.001   TRP K 662 
 HIS   0.006   0.001   HIS K 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7520)
  covalent geometry    : angle       0.62162 (10188)
  hydrogen bonds       : bond        0.03585 (  348)
  hydrogen bonds       : angle       4.22541 (  978)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1141.85 seconds
wall clock time: 20 minutes 25.13 seconds (1225.13 seconds total)