Starting phenix.real_space_refine
on Fri Aug  7 17:56:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8psz_17865/08_2026/8psz_17865_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8psz_17865/08_2026/8psz_17865.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8psz_17865/08_2026/8psz_17865_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8psz_17865/08_2026/8psz_17865_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8psz_17865/08_2026/8psz_17865.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8psz_17865/08_2026/8psz_17865.map"
  }
  resolution = 2.42
  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: 8
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     P      56      5.49       5
     Mg      2      5.21       5
     S      63      5.16       5
     C    7221      2.51       5
     N    2077      2.21       5
     O    2481      1.98       5
     H   11195      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 23098
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 6653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 6653
          Classifications: {'peptide': 417}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 394}
    Chain: "B"
      Number of atoms: 7958
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 513, 7925
          Classifications: {'peptide': 513}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 491}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 513, 7925
          Classifications: {'peptide': 513}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 491}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7960
    Chain: "C"
      Number of atoms: 6652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 6652
          Classifications: {'peptide': 425}
          Link IDs: {'PTRANS': 22, 'TRANS': 402}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "V"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 406
          Classifications: {'RNA': 13}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 5, 'rna3p': 7}
    Chain: "S"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 422
          Classifications: {'RNA': 13}
          Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4}
          Link IDs: {'rna3p': 12}
    Chain: "P"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 411
          Classifications: {'RNA': 13}
          Modifications used: {'3*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 12}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 453
          Classifications: {'RNA': 14}
          Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 4, 'rna3p': 9}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 31
          Unusual residues: {' MG': 2, 'A0I': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 42
          Classifications: {'water': 42}
          Link IDs: {None: 41}
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 40
          Classifications: {'water': 40}
          Link IDs: {None: 39}
    Chain: "C"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "V"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 14
          Classifications: {'water': 14}
          Link IDs: {None: 13}
    Chain: "S"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2585  SG  CYS A 161      46.840  53.436  18.382  1.00 20.80           S
  ATOM   4474  SG  CYS A 282      44.558  52.018  15.484  1.00 21.12           S
  ATOM  18191  SG  CYS C 233      23.667  63.533 108.687  1.00 68.90           S
  ATOM  18215  SG  CYS C 235      23.744  64.404 104.935  1.00 63.55           S
  ATOM  16857  SG  CYS C 146      12.028  72.706  88.850  1.00 71.81           S
  ATOM  17045  SG  CYS C 159      13.000  75.499  90.912  1.00 66.96           S
  ATOM  17101  SG  CYS C 163      15.366  72.687  90.646  1.00 60.91           S
  ATOM  17111  SG  CYS C 164      14.711  75.039  87.428  1.00 64.71           S

  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AASP B 213 " occ=0.50
      ... (22 atoms not shown)
      pdb=" HB3BASP B 213 " occ=0.50
    residue:
      pdb=" N  ATYR B 393 " occ=0.60
      ... (40 atoms not shown)
      pdb=" HH BTYR B 393 " occ=0.40
  Time building chain proxies: 5.42, per 1000 atoms: 0.23
  Number of scatterers: 23098
  At special positions: 0
  Unit cell: (92.4, 109.2, 125.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      3     29.99
     S      63     16.00
     P      56     15.00
     Mg      2     11.99
     O    2481      8.00
     N    2077      7.00
     C    7221      6.00
     H   11195      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.12
  Conformation dependent library (CDL) restraints added in 836.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" ND1 HIS A 284 "
        pdb="ZN    ZN A 501 " - pdb=" NE2 HIS A 296 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 161 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 282 "
      pdb="  ZN C 501 "
        pdb="ZN    ZN C 501 " - pdb=" NE2 HIS C 191 "
        pdb="ZN    ZN C 501 " - pdb=" ND1 HIS C 184 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 233 "
        pdb="ZN    ZN C 501 " - pdb=" SG  CYS C 235 "
      pdb="  ZN C 502 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 146 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 159 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 163 "
        pdb="ZN    ZN C 502 " - pdb=" SG  CYS C 164 "
      Number of angles added : 9


  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2548

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 15 sheets defined
      42.4% alpha, 13.9% beta
      15 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 3.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 4
      No H-bonds generated for 'chain 'A' and resid 2 through 4'
    Processing helix  chain 'A' and resid 5 through 13
    Processing helix  chain 'A' and resid 83 through 94
    Processing helix  chain 'A' and resid 112 through 123
    Processing helix  chain 'A' and resid 141 through 157
    Processing helix  chain 'A' and resid 162 through 169
    Processing helix  chain 'A' and resid 174 through 189
    Processing helix  chain 'A' and resid 223 through 234
    Processing helix  chain 'A' and resid 301 through 311
      removed outlier: 3.878A  pdb=" N   GLN A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 322
    Processing helix  chain 'A' and resid 344 through 356
      removed outlier: 3.523A  pdb=" N   VAL A 348 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 374
      removed outlier: 3.967A  pdb=" N   ALA A 363 " --> pdb=" O   ARG A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 386
    Processing helix  chain 'A' and resid 388 through 392
      removed outlier: 3.555A  pdb=" N   ILE A 392 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 415
    Processing helix  chain 'B' and resid 1 through 5
    Processing helix  chain 'B' and resid 23 through 39
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 3.501A  pdb=" N   TYR B  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 103
    Processing helix  chain 'B' and resid 107 through 118
    Processing helix  chain 'B' and resid 129 through 138
      removed outlier: 3.648A  pdb=" N   ARG B 138 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 183
      removed outlier: 3.646A  pdb=" N   VAL B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 203
    Processing helix  chain 'B' and resid 204 through 206
      No H-bonds generated for 'chain 'B' and resid 204 through 206'
    Processing helix  chain 'B' and resid 222 through 234
    Processing helix  chain 'B' and resid 235 through 248
    Processing helix  chain 'B' and resid 269 through 279
      removed outlier: 3.728A  pdb=" N   LEU B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 311
    Processing helix  chain 'B' and resid 354 through 372
      removed outlier: 3.972A  pdb=" N   LEU B 359 " --> pdb=" O   PRO B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 396
    Processing helix  chain 'B' and resid 409 through 413
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 429 through 436
      removed outlier: 4.035A  pdb=" N   GLN B 434 " --> pdb=" O   PHE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 454
    Processing helix  chain 'B' and resid 479 through 497
    Processing helix  chain 'B' and resid 506 through 513
    Processing helix  chain 'C' and resid 3 through 8
    Processing helix  chain 'C' and resid 16 through 23
    Processing helix  chain 'C' and resid 33 through 40
    Processing helix  chain 'C' and resid 42 through 54
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'C' and resid 87 through 97
    Processing helix  chain 'C' and resid 100 through 107
    Processing helix  chain 'C' and resid 145 through 151
      removed outlier: 3.736A  pdb=" N   VAL C 151 " --> pdb=" O   GLU C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 161 through 165
      removed outlier: 3.549A  pdb=" N   GLY C 165 " --> pdb=" O   ILE C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 219
    Processing helix  chain 'C' and resid 234 through 241
    Processing helix  chain 'C' and resid 281 through 289
    Processing helix  chain 'C' and resid 303 through 316
    Processing helix  chain 'C' and resid 319 through 334
    Processing helix  chain 'C' and resid 350 through 356
    Processing helix  chain 'C' and resid 370 through 375
    Processing helix  chain 'C' and resid 421 through 426
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.627A  pdb=" N   TRP A  52 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   CYS A  71 " --> pdb=" O   TRP A  52 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ALA A  54 " --> pdb=" O   CYS A  71 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   LEU A  73 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   GLU A  56 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   THR A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137
      removed outlier: 3.540A  pdb=" N   PHE B 291 " --> pdb=" O   GLY B 212 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.302A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194
      removed outlier: 6.302A  pdb=" N   TRP A 198 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LEU A 277 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   HIS A 271 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 79
    Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 159
      removed outlier: 7.129A  pdb=" N   PHE B 140 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329
    Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478
    Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83
    Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 224
      removed outlier: 6.779A  pdb=" N   GLY C 262 " --> pdb=" O   PHE C 258 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 360 through 363
    Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 388
      removed outlier: 6.623A  pdb=" N   MET C 415 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)

    495 hydrogen bonds defined for protein.
    1342 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      34 hydrogen bonds
      68 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 4.67

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 11163
        1.03 -     1.23: 52
        1.23 -     1.42: 5191
        1.42 -     1.62: 6842
        1.62 -     1.81: 89
  Bond restraints: 23337
  Sorted by residual:
  bond pdb=" O7  A0I B 601 "
       pdb=" P3  A0I B 601 "
    ideal  model  delta    sigma   weight residual
    1.731  1.618  0.113 2.00e-02 2.50e+03 3.16e+01
  bond pdb=" C   PRO C 234 "
       pdb=" O   PRO C 234 "
    ideal  model  delta    sigma   weight residual
    1.235  1.177  0.058 1.30e-02 5.92e+03 1.98e+01
  bond pdb=" N4  A0I B 601 "
       pdb=" P2  A0I B 601 "
    ideal  model  delta    sigma   weight residual
    1.701  1.641  0.060 2.00e-02 2.50e+03 8.89e+00
  bond pdb=" O3  A0I B 601 "
       pdb=" P1  A0I B 601 "
    ideal  model  delta    sigma   weight residual
    1.662  1.603  0.059 2.00e-02 2.50e+03 8.82e+00
  bond pdb=" N4  A0I B 601 "
       pdb=" P1  A0I B 601 "
    ideal  model  delta    sigma   weight residual
    1.691  1.642  0.049 2.00e-02 2.50e+03 5.88e+00
  ... (remaining 23332 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 41406
        1.62 -     3.25: 667
        3.25 -     4.87: 47
        4.87 -     6.50: 2
        6.50 -     8.12: 1
  Bond angle restraints: 42123
  Sorted by residual:
  angle pdb=" O5'   A S  32 "
        pdb=" C5'   A S  32 "
        pdb=" C4'   A S  32 "
      ideal   model   delta    sigma   weight residual
     109.40  112.83   -3.43 8.00e-01 1.56e+00 1.84e+01
  angle pdb=" O5'   A S  33 "
        pdb=" C5'   A S  33 "
        pdb=" C4'   A S  33 "
      ideal   model   delta    sigma   weight residual
     109.40  112.21   -2.81 8.00e-01 1.56e+00 1.23e+01
  angle pdb=" O5'   G D  16 "
        pdb=" C5'   G D  16 "
        pdb=" C4'   G D  16 "
      ideal   model   delta    sigma   weight residual
     109.40  112.05   -2.65 8.00e-01 1.56e+00 1.09e+01
  angle pdb=" O5'   C V  15 "
        pdb=" C5'   C V  15 "
        pdb=" C4'   C V  15 "
      ideal   model   delta    sigma   weight residual
     109.40  111.97   -2.57 8.00e-01 1.56e+00 1.03e+01
  angle pdb=" O5'   U P  18 "
        pdb=" C5'   U P  18 "
        pdb=" C4'   U P  18 "
      ideal   model   delta    sigma   weight residual
     109.40  111.97   -2.57 8.00e-01 1.56e+00 1.03e+01
  ... (remaining 42118 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 9721
       17.80 -    35.60: 836
       35.60 -    53.41: 342
       53.41 -    71.21: 120
       71.21 -    89.01: 29
  Dihedral angle restraints: 11048
    sinusoidal: 6454
      harmonic: 4594
  Sorted by residual:
  dihedral pdb=" CD  ARG B 176 "
           pdb=" NE  ARG B 176 "
           pdb=" CZ  ARG B 176 "
           pdb=" NH1 ARG B 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   41.02  -41.02     1      1.00e+01 1.00e-02 2.36e+01
  dihedral pdb=" CA  ARG B 394 "
           pdb=" C   ARG B 394 "
           pdb=" N   TYR B 395 "
           pdb=" CA  TYR B 395 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.02  -21.98     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  SER B 286 "
           pdb=" C   SER B 286 "
           pdb=" N   PHE B 287 "
           pdb=" CA  PHE B 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.83   19.17     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 11045 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1532
       0.044 -    0.088: 234
       0.088 -    0.132: 134
       0.132 -    0.176: 0
       0.176 -    0.220: 1
  Chirality restraints: 1901
  Sorted by residual:
  chirality pdb=" C7  A0I B 601 "
            pdb=" C6  A0I B 601 "
            pdb=" C8  A0I B 601 "
            pdb=" O12 A0I B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.37   -2.59    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  VAL C 221 "
            pdb=" N   VAL C 221 "
            pdb=" C   VAL C 221 "
            pdb=" CB  VAL C 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  VAL A 252 "
            pdb=" N   VAL A 252 "
            pdb=" C   VAL A 252 "
            pdb=" CB  VAL A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.15e-01
  ... (remaining 1898 not shown)

  Planarity restraints: 3274
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 176 "    0.749 9.50e-02 1.11e+02   2.50e-01 6.59e+01
        pdb=" NE  ARG B 176 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 176 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 176 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 176 "    0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG B 176 "   -0.012 2.00e-02 2.50e+03
        pdb="HH12 ARG B 176 "    0.010 2.00e-02 2.50e+03
        pdb="HH21 ARG B 176 "   -0.003 2.00e-02 2.50e+03
        pdb="HH22 ARG B 176 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   3 "   -0.022 2.00e-02 2.50e+03   9.08e-03 2.68e+00
        pdb=" N9    A V   3 "    0.022 2.00e-02 2.50e+03
        pdb=" C8    A V   3 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A V   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A V   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A V   3 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A V   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A V   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A V   3 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A V   3 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A V   3 "    0.003 2.00e-02 2.50e+03
        pdb=" H8    A V   3 "    0.002 2.00e-02 2.50e+03
        pdb=" H2    A V   3 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 161 "   -0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO B 162 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B 162 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 162 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 3271 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 898
        2.16 -     2.77: 43029
        2.77 -     3.38: 65847
        3.38 -     3.99: 89220
        3.99 -     4.60: 135252
  Nonbonded interactions: 334246
  Sorted by model distance:
  nonbonded pdb=" O   SER A 128 "
            pdb="HD22 ASN B  44 "
     model   vdw
     1.549 2.450
  nonbonded pdb=" H   GLY A 239 "
            pdb=" O   ALA A 251 "
     model   vdw
     1.582 2.450
  nonbonded pdb=" OD1 ASN B 397 "
            pdb=" HG1 THR B 399 "
     model   vdw
     1.590 2.450
  nonbonded pdb=" H   GLY C  85 "
            pdb=" OD1 ASP C 110 "
     model   vdw
     1.630 2.450
  nonbonded pdb=" HG1 THR B 103 "
            pdb=" O   ILE B 125 "
     model   vdw
     1.631 2.450
  ... (remaining 334241 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'D' and resid 5 through 17)
  selection = (chain 'S' and (resid 28 through 34 or resid 36 through 40))
}

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=0.40 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.170
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     30.530
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
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   0.113  12154  Z= 0.150
  Angle     :  0.541   9.351  16675  Z= 0.329
  Chirality :  0.040   0.220   1901
  Planarity :  0.008   0.321   1951
  Dihedral  : 17.754  89.008   4872
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.38 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.23), residues: 1351
  helix:  1.65 (0.23), residues: 525
  sheet:  0.20 (0.40), residues: 148
  loop : -0.07 (0.24), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  83 
 TYR   0.012   0.001   TYR C 315 
 PHE   0.009   0.001   PHE C  44 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.15 (12142)
  covalent geometry    : angle       0.52901 /  0.33 (16666)
  hydrogen bonds       : bond        0.12888 /  8.87 (  514)
  hydrogen bonds       : angle       5.58584 /  4.02 ( 1410)
  metal coordination   : bond        0.00840 /  0.42 (   12)
  metal coordination   : angle       4.80964 /  2.14 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 173
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 LYS cc_start: 0.8594 (mttt) cc_final: 0.8363 (mttp)
REVERT: A  332 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7873 (mtp180)
REVERT: B  282 ASP cc_start: 0.8477 (p0) cc_final: 0.8276 (p0)
REVERT: B  480 GLU cc_start: 0.7593 (tt0) cc_final: 0.7385 (tt0)
REVERT: C   77 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8663 (ptt90)
REVERT: C   89 GLU cc_start: 0.7603 (mp0) cc_final: 0.7392 (mp0)
REVERT: C  109 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7065 (mp10)
REVERT: C  348 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7637 (mppt)
REVERT: C  351 ILE cc_start: 0.7809 (mm) cc_final: 0.7532 (mm)
REVERT: C  413 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7524 (mtmt)
REVERT: C  427 LYS cc_start: 0.7300 (ttmt) cc_final: 0.7088 (tttm)
  outliers start: 24
  outliers final: 9
  residues processed: 194
  average time/residue: 1.4774
  time to fit residues: 305.7143
Evaluate side-chains
  128 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 CYS
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain C residue  388 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0370
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7260

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 200 GLN
B  44 ASN
C 284 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.116504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.086570 restraints weight = 45621.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 1.69
r_work: 0.2822 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.2714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.1108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  12154  Z= 0.121
  Angle     :  0.507   5.050  16675  Z= 0.270
  Chirality :  0.037   0.140   1901
  Planarity :  0.005   0.118   1951
  Dihedral  : 13.087  73.681   2316
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 16.12 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.23), residues: 1351
  helix:  1.77 (0.23), residues: 530
  sheet: -0.02 (0.40), residues: 145
  loop : -0.03 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 176 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 (12142)
  covalent geometry    : angle       0.50337 /  0.27 (16666)
  hydrogen bonds       : bond        0.05106 /  3.34 (  514)
  hydrogen bonds       : angle       4.74165 /  3.44 ( 1410)
  metal coordination   : bond        0.00429 /  0.26 (   12)
  metal coordination   : angle       2.69561 /  1.21 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.6460 (m110) cc_final: 0.6132 (m110)
REVERT: A  279 LYS cc_start: 0.8708 (mttt) cc_final: 0.8361 (mttp)
REVERT: B  176 ARG cc_start: 0.8303 (ttm110) cc_final: 0.8065 (ttp-170)
REVERT: B  480 GLU cc_start: 0.7796 (tt0) cc_final: 0.7461 (tt0)
REVERT: C   77 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8609 (ptt90)
REVERT: C   89 GLU cc_start: 0.7408 (mp0) cc_final: 0.7021 (mp0)
REVERT: C  109 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7053 (mp10)
REVERT: C  196 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6544 (mt-10)
REVERT: C  348 LYS cc_start: 0.8124 (mmtp) cc_final: 0.7478 (mppt)
REVERT: C  413 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7786 (mtmt)
REVERT: C  427 LYS cc_start: 0.7451 (ttmt) cc_final: 0.7133 (tttm)
  outliers start: 19
  outliers final: 10
  residues processed: 139
  average time/residue: 1.5214
  time to fit residues: 224.8111
Evaluate side-chains
  132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 CYS
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  356 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 107 optimal weight:    0.3980
   chunk 52 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 119 optimal weight:    4.9990
   chunk 112 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0870
   overall best weight:    0.8562

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.116276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.085919 restraints weight = 51951.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 1.79
r_work: 0.2811 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2705 r_free = 0.2705    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8853
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  12154  Z= 0.115
  Angle     :  0.481   5.135  16675  Z= 0.255
  Chirality :  0.036   0.138   1901
  Planarity :  0.004   0.060   1951
  Dihedral  : 12.937  73.599   2312
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 16.47 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.23), residues: 1351
  helix:  1.81 (0.23), residues: 530
  sheet: -0.03 (0.41), residues: 145
  loop : -0.04 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  83 
 TYR   0.014   0.001   TYR A 403 
 PHE   0.011   0.001   PHE C  44 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 (12142)
  covalent geometry    : angle       0.47765 /  0.26 (16666)
  hydrogen bonds       : bond        0.04765 /  3.11 (  514)
  hydrogen bonds       : angle       4.57809 /  3.32 ( 1410)
  metal coordination   : bond        0.00377 /  0.23 (   12)
  metal coordination   : angle       2.30336 /  1.02 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.6530 (m110) cc_final: 0.6234 (m110)
REVERT: B  480 GLU cc_start: 0.7827 (tt0) cc_final: 0.7477 (tt0)
REVERT: C   77 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8685 (ptt90)
REVERT: C   89 GLU cc_start: 0.7351 (mp0) cc_final: 0.7074 (mp0)
REVERT: C  109 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7089 (mp10)
REVERT: C  170 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6414 (mtpt)
REVERT: C  196 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6593 (mt-10)
REVERT: C  348 LYS cc_start: 0.8122 (mmtp) cc_final: 0.7482 (mppt)
  outliers start: 15
  outliers final: 9
  residues processed: 136
  average time/residue: 1.7617
  time to fit residues: 253.9754
Evaluate side-chains
  129 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  386 ILE
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  170 LYS
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  300 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 51 optimal weight:    0.2980
   chunk 47 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 134 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 109 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.117250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.087026 restraints weight = 48391.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 1.74
r_work: 0.2827 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  12154  Z= 0.097
  Angle     :  0.466   5.175  16675  Z= 0.246
  Chirality :  0.036   0.139   1901
  Planarity :  0.004   0.054   1951
  Dihedral  : 12.787  73.540   2311
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.55 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.23), residues: 1351
  helix:  1.92 (0.23), residues: 530
  sheet: -0.05 (0.41), residues: 145
  loop : -0.02 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  83 
 TYR   0.013   0.001   TYR A 403 
 PHE   0.009   0.001   PHE C 175 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00208 /  0.10 (12142)
  covalent geometry    : angle       0.46365 /  0.25 (16666)
  hydrogen bonds       : bond        0.04205 /  2.71 (  514)
  hydrogen bonds       : angle       4.41955 /  3.21 ( 1410)
  metal coordination   : bond        0.00318 /  0.19 (   12)
  metal coordination   : angle       1.92914 /  0.85 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.6613 (m110) cc_final: 0.6324 (m110)
REVERT: A  279 LYS cc_start: 0.8698 (mttt) cc_final: 0.8353 (mttp)
REVERT: B   53 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7394 (pptt)
REVERT: B  480 GLU cc_start: 0.7812 (tt0) cc_final: 0.7443 (tt0)
REVERT: C   77 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8628 (ptt90)
REVERT: C   89 GLU cc_start: 0.7259 (mp0) cc_final: 0.7035 (mp0)
REVERT: C  109 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7073 (mp10)
REVERT: C  170 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6285 (mtpt)
REVERT: C  196 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6555 (mt-10)
REVERT: C  348 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7418 (mppt)
  outliers start: 17
  outliers final: 11
  residues processed: 130
  average time/residue: 1.8357
  time to fit residues: 252.6106
Evaluate side-chains
  131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   53 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  170 LYS
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  197 ASP
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  317 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 135 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9980
   chunk 109 optimal weight:    0.5980
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.8382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.116783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.086027 restraints weight = 56364.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 1.87
r_work: 0.2807 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8856
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  12154  Z= 0.111
  Angle     :  0.466   5.199  16675  Z= 0.247
  Chirality :  0.036   0.136   1901
  Planarity :  0.004   0.052   1951
  Dihedral  : 12.709  73.620   2310
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.95 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.23), residues: 1351
  helix:  1.97 (0.23), residues: 530
  sheet: -0.06 (0.40), residues: 145
  loop : -0.06 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  83 
 TYR   0.015   0.001   TYR A 403 
 PHE   0.010   0.001   PHE C  44 
 TRP   0.006   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 (12142)
  covalent geometry    : angle       0.46326 /  0.25 (16666)
  hydrogen bonds       : bond        0.04288 /  2.78 (  514)
  hydrogen bonds       : angle       4.36546 /  3.17 ( 1410)
  metal coordination   : bond        0.00404 /  0.27 (   12)
  metal coordination   : angle       2.04554 /  0.92 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLU cc_start: 0.8056 (tp30) cc_final: 0.7565 (tp30)
REVERT: A  279 LYS cc_start: 0.8706 (mttt) cc_final: 0.8357 (mttp)
REVERT: A  323 ASP cc_start: 0.7950 (t0) cc_final: 0.7706 (t0)
REVERT: B   53 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7523 (pptt)
REVERT: B  159 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.8947 (mt)
REVERT: B  480 GLU cc_start: 0.7838 (tt0) cc_final: 0.7454 (tt0)
REVERT: B  495 LYS cc_start: 0.7618 (ttpp) cc_final: 0.7413 (tmmt)
REVERT: C   77 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8689 (ptt90)
REVERT: C   80 LEU cc_start: 0.8731 (tp) cc_final: 0.8385 (tp)
REVERT: C   89 GLU cc_start: 0.7236 (mp0) cc_final: 0.6982 (mp0)
REVERT: C  109 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7062 (mp10)
REVERT: C  196 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6566 (mt-10)
REVERT: C  348 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7419 (mppt)
  outliers start: 21
  outliers final: 12
  residues processed: 132
  average time/residue: 1.7258
  time to fit residues: 241.8603
Evaluate side-chains
  131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue  278 SER
Chi-restraints excluded: chain A residue  332 ARG
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   53 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  197 ASP
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  356 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 134 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  44 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.114472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.084148 restraints weight = 48247.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 1.72
r_work: 0.2777 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12154  Z= 0.198
  Angle     :  0.533   5.432  16675  Z= 0.284
  Chirality :  0.039   0.137   1901
  Planarity :  0.005   0.054   1951
  Dihedral  : 12.876  73.692   2310
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.69 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.22), residues: 1351
  helix:  1.73 (0.23), residues: 530
  sheet: -0.23 (0.39), residues: 150
  loop : -0.18 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 155 
 TYR   0.018   0.002   TYR A 403 
 PHE   0.018   0.002   PHE C  44 
 TRP   0.008   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 371 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00445 /  0.20 (12142)
  covalent geometry    : angle       0.52907 /  0.28 (16666)
  hydrogen bonds       : bond        0.05217 /  3.42 (  514)
  hydrogen bonds       : angle       4.53898 /  3.27 ( 1410)
  metal coordination   : bond        0.00814 /  0.53 (   12)
  metal coordination   : angle       2.82987 /  1.29 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 LYS cc_start: 0.8674 (mttt) cc_final: 0.8394 (mttp)
REVERT: A  323 ASP cc_start: 0.8306 (t0) cc_final: 0.8071 (t0)
REVERT: B  480 GLU cc_start: 0.7895 (tt0) cc_final: 0.7540 (tt0)
REVERT: B  495 LYS cc_start: 0.7662 (ttpp) cc_final: 0.7448 (tmmt)
REVERT: C   89 GLU cc_start: 0.7240 (mp0) cc_final: 0.7039 (mp0)
REVERT: C  109 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7069 (mp10)
REVERT: C  196 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6518 (mt-10)
REVERT: C  348 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7512 (mppt)
  outliers start: 24
  outliers final: 17
  residues processed: 137
  average time/residue: 1.6392
  time to fit residues: 239.0838
Evaluate side-chains
  131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   53 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  386 ILE
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  197 ASP
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 135 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0670
   chunk 126 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1924

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  44 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.115266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.085395 restraints weight = 43824.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 1.64
r_work: 0.2801 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12154  Z= 0.135
  Angle     :  0.499   5.459  16675  Z= 0.265
  Chirality :  0.037   0.140   1901
  Planarity :  0.004   0.050   1951
  Dihedral  : 12.723  73.595   2302
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.47 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.22), residues: 1351
  helix:  1.78 (0.23), residues: 530
  sheet: -0.18 (0.40), residues: 145
  loop : -0.15 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  83 
 TYR   0.015   0.001   TYR A 403 
 PHE   0.014   0.001   PHE C  44 
 TRP   0.009   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.14 (12142)
  covalent geometry    : angle       0.49522 /  0.26 (16666)
  hydrogen bonds       : bond        0.04701 /  3.06 (  514)
  hydrogen bonds       : angle       4.48510 /  3.24 ( 1410)
  metal coordination   : bond        0.00540 /  0.32 (   12)
  metal coordination   : angle       2.54092 /  1.14 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 LYS cc_start: 0.8659 (mttt) cc_final: 0.8382 (mttp)
REVERT: A  323 ASP cc_start: 0.8202 (t0) cc_final: 0.7980 (t0)
REVERT: B   53 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7559 (pptt)
REVERT: B  159 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.8940 (mt)
REVERT: B  480 GLU cc_start: 0.7868 (tt0) cc_final: 0.7522 (tt0)
REVERT: C  109 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7066 (mp10)
REVERT: C  196 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6474 (mt-10)
REVERT: C  348 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7493 (mppt)
  outliers start: 17
  outliers final: 13
  residues processed: 125
  average time/residue: 1.8614
  time to fit residues: 247.5558
Evaluate side-chains
  129 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   53 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  197 ASP
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  44 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.114425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.083760 restraints weight = 51162.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 1.78
r_work: 0.2774 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12154  Z= 0.189
  Angle     :  0.529   5.554  16675  Z= 0.282
  Chirality :  0.038   0.137   1901
  Planarity :  0.005   0.051   1951
  Dihedral  : 12.783  73.628   2302
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.38 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.22), residues: 1351
  helix:  1.65 (0.22), residues: 530
  sheet: -0.24 (0.41), residues: 133
  loop : -0.22 (0.23), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  29 
 TYR   0.017   0.002   TYR A 403 
 PHE   0.017   0.002   PHE C  44 
 TRP   0.009   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.19 (12142)
  covalent geometry    : angle       0.52560 /  0.28 (16666)
  hydrogen bonds       : bond        0.05134 /  3.36 (  514)
  hydrogen bonds       : angle       4.56512 /  3.29 ( 1410)
  metal coordination   : bond        0.00766 /  0.49 (   12)
  metal coordination   : angle       2.71890 /  1.22 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 LYS cc_start: 0.8682 (mttt) cc_final: 0.8402 (mttp)
REVERT: A  323 ASP cc_start: 0.8353 (t0) cc_final: 0.8090 (t0)
REVERT: B  159 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.8938 (mt)
REVERT: B  480 GLU cc_start: 0.7932 (tt0) cc_final: 0.7603 (tt0)
REVERT: C  109 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7082 (mp10)
REVERT: C  196 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6508 (mt-10)
REVERT: C  348 LYS cc_start: 0.8166 (mmtp) cc_final: 0.7520 (mppt)
  outliers start: 18
  outliers final: 16
  residues processed: 127
  average time/residue: 1.8217
  time to fit residues: 246.6198
Evaluate side-chains
  132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   53 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  197 ASP
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  44 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.115115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.084555 restraints weight = 50628.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 1.77
r_work: 0.2787 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2676 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2676 r_free = 0.2676    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8881
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12154  Z= 0.143
  Angle     :  0.503   5.627  16675  Z= 0.267
  Chirality :  0.037   0.140   1901
  Planarity :  0.005   0.057   1951
  Dihedral  : 12.738  73.612   2302
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.47 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.22), residues: 1351
  helix:  1.72 (0.23), residues: 530
  sheet: -0.20 (0.40), residues: 145
  loop : -0.17 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  83 
 TYR   0.015   0.001   TYR A 403 
 PHE   0.013   0.001   PHE C  44 
 TRP   0.009   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 (12142)
  covalent geometry    : angle       0.49922 /  0.27 (16666)
  hydrogen bonds       : bond        0.04734 /  3.08 (  514)
  hydrogen bonds       : angle       4.50188 /  3.25 ( 1410)
  metal coordination   : bond        0.00612 /  0.37 (   12)
  metal coordination   : angle       2.55598 /  1.13 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 LYS cc_start: 0.8675 (mttt) cc_final: 0.8399 (mttp)
REVERT: A  323 ASP cc_start: 0.8267 (t0) cc_final: 0.8038 (t0)
REVERT: B   53 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7534 (pptt)
REVERT: B  159 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.8933 (mt)
REVERT: B  480 GLU cc_start: 0.7926 (tt0) cc_final: 0.7623 (tt0)
REVERT: C  109 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7086 (mp10)
REVERT: C  196 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6542 (mt-10)
REVERT: C  348 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7497 (mppt)
  outliers start: 17
  outliers final: 14
  residues processed: 129
  average time/residue: 1.7830
  time to fit residues: 244.6696
Evaluate side-chains
  132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   53 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  197 ASP
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0020
   chunk 128 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.1794

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.115484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.085751 restraints weight = 41894.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 1.61
r_work: 0.2809 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12154  Z= 0.134
  Angle     :  0.493   5.622  16675  Z= 0.262
  Chirality :  0.037   0.139   1901
  Planarity :  0.004   0.054   1951
  Dihedral  : 12.688  73.604   2302
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.47 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.22), residues: 1351
  helix:  1.76 (0.23), residues: 530
  sheet: -0.17 (0.40), residues: 145
  loop : -0.15 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  29 
 TYR   0.014   0.001   TYR A 403 
 PHE   0.012   0.001   PHE C  44 
 TRP   0.008   0.001   TRP A 346 
 HIS   0.004   0.001   HIS B 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 (12142)
  covalent geometry    : angle       0.48979 /  0.26 (16666)
  hydrogen bonds       : bond        0.04572 /  2.96 (  514)
  hydrogen bonds       : angle       4.44722 /  3.22 ( 1410)
  metal coordination   : bond        0.00550 /  0.35 (   12)
  metal coordination   : angle       2.44715 /  1.09 (    9)

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

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

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2702 Ramachandran restraints generated.
    1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 LYS cc_start: 0.8668 (mttt) cc_final: 0.8392 (mttp)
REVERT: B   53 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7509 (pptt)
REVERT: B  159 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.8924 (mt)
REVERT: B  480 GLU cc_start: 0.7884 (tt0) cc_final: 0.7585 (tt0)
REVERT: C  109 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7073 (mp10)
REVERT: C  196 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6520 (mt-10)
REVERT: C  348 LYS cc_start: 0.8136 (mmtp) cc_final: 0.7483 (mppt)
  outliers start: 17
  outliers final: 14
  residues processed: 131
  average time/residue: 1.6098
  time to fit residues: 224.7822
Evaluate side-chains
  132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 THR
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   53 LYS
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  444 ASP
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue   81 SER
Chi-restraints excluded: chain C residue  196 GLU
Chi-restraints excluded: chain C residue  197 ASP
Chi-restraints excluded: chain C residue  300 VAL
Chi-restraints excluded: chain C residue  301 SER
Chi-restraints excluded: chain C residue  322 SER
Chi-restraints excluded: chain C residue  356 SER
Chi-restraints excluded: chain C residue  358 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 11 optimal weight:    0.2980
   chunk 103 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0020
   chunk 7 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 88 optimal weight:    0.4980
   chunk 19 optimal weight:    0.4980
   chunk 110 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 389 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.117398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.087424 restraints weight = 45766.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.69
r_work: 0.2838 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12154  Z= 0.092
  Angle     :  0.471   5.985  16675  Z= 0.247
  Chirality :  0.036   0.143   1901
  Planarity :  0.004   0.054   1951
  Dihedral  : 12.551  73.511   2302
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 17.32 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.23), residues: 1351
  helix:  1.95 (0.23), residues: 530
  sheet: -0.06 (0.40), residues: 143
  loop : -0.09 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  83 
 TYR   0.011   0.001   TYR A 403 
 PHE   0.010   0.001   PHE B 287 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00199 /  0.09 (12142)
  covalent geometry    : angle       0.46873 /  0.25 (16666)
  hydrogen bonds       : bond        0.03890 /  2.49 (  514)
  hydrogen bonds       : angle       4.29889 /  3.12 ( 1410)
  metal coordination   : bond        0.00398 /  0.28 (   12)
  metal coordination   : angle       2.11422 /  0.93 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9668.94 seconds
wall clock time: 163 minutes 59.04 seconds (9839.04 seconds total)