Starting phenix.real_space_refine
on Tue Feb  3 21:27:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ek0_48111/02_2026/9ek0_48111.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ek0_48111/02_2026/9ek0_48111.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ek0_48111/02_2026/9ek0_48111.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ek0_48111/02_2026/9ek0_48111.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ek0_48111/02_2026/9ek0_48111.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ek0_48111/02_2026/9ek0_48111.map"
  }
  resolution = 2.79
  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=   0.007 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4485      2.51       5
     N    1215      2.21       5
     O    1300      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7050
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2231
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 2606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2606
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "A"
      Number of atoms: 1763
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 213, 1756
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 213, 1756
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 1778
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'IXO': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APRO A 326 " occ=0.58
      ... (12 atoms not shown)
      pdb=" CD BPRO A 326 " occ=0.42
  Time building chain proxies: 1.57, per 1000 atoms: 0.22
  Number of scatterers: 7050
  At special positions: 0
  Unit cell: (85.15, 93.6, 129.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1300      8.00
     N    1215      7.00
     C    4485      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 103 " - pdb=" SG  CYS R 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 468 " - pdb=" SG  CYS R 471 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 240.6 milliseconds
  

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      47.0% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'R' and resid 26 through 57
    Processing helix  chain 'R' and resid 65 through 94
      removed outlier: 4.093A  pdb=" N   LEU R  69 " --> pdb=" O   ASN R  65 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   MET R  84 " --> pdb=" O   GLY R  80 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   ASN R  85 " --> pdb=" O   ILE R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 99 through 134
    Processing helix  chain 'R' and resid 137 through 141
      removed outlier: 3.604A  pdb=" N   ALA R 140 " --> pdb=" O   THR R 137 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 143 through 168
      Proline residue:  R 164  - end of helix
    Processing helix  chain 'R' and resid 168 through 174
    Processing helix  chain 'R' and resid 185 through 189
      removed outlier: 3.849A  pdb=" N   LEU R 188 " --> pdb=" O   ILE R 185 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER R 189 " --> pdb=" O   GLN R 186 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 185 through 189'
    Processing helix  chain 'R' and resid 190 through 200
    Processing helix  chain 'R' and resid 202 through 231
    Processing helix  chain 'R' and resid 439 through 466
      removed outlier: 3.984A  pdb=" N   LEU R 444 " --> pdb=" O   ALA R 440 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   SER R 445 " --> pdb=" O   ALA R 441 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU R 448 " --> pdb=" O   LEU R 444 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU R 449 " --> pdb=" O   SER R 445 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   THR R 454 " --> pdb=" O   ALA R 450 " (cutoff:3.500A)
      Proline residue:  R 457  - end of helix
      removed outlier: 4.125A  pdb=" N   LEU R 463 " --> pdb=" O   ASN R 459 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 473 through 496
      removed outlier: 3.807A  pdb=" N   TYR R 485 " --> pdb=" O   TYR R 481 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   SER R 488 " --> pdb=" O   CYS R 484 " (cutoff:3.500A)
      Proline residue:  R 492  - end of helix
    Processing helix  chain 'R' and resid 499 through 512
      removed outlier: 4.235A  pdb=" N   LEU R 511 " --> pdb=" O   LYS R 507 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   CYS R 512 " --> pdb=" O   MET R 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'A' and resid 19 through 39
      removed outlier: 3.593A  pdb=" N   LYS A  36 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.604A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.892A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.547A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.531A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.611A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.012A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.752A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.883A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.680A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.576A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.457A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 208 through 214
      removed outlier: 9.409A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1098 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.85

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1147
        1.31 -     1.43: 1943
        1.43 -     1.56: 4027
        1.56 -     1.68: 2
        1.68 -     1.81: 70
  Bond restraints: 7189
  Sorted by residual:
  bond pdb=" N11 IXO R 601 "
       pdb=" O12 IXO R 601 "
    ideal  model  delta    sigma   weight residual
    1.385  1.429 -0.044 2.00e-02 2.50e+03 4.92e+00
  bond pdb=" C   ASN R 491 "
       pdb=" N   PRO R 492 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.027 1.30e-02 5.92e+03 4.42e+00
  bond pdb=" C   THR R 456 "
       pdb=" N   PRO R 457 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.027 1.28e-02 6.10e+03 4.36e+00
  bond pdb=" C   ILE R 204 "
       pdb=" N   PRO R 205 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.36e-02 5.41e+03 3.05e+00
  bond pdb=" C   GLU A 327 "
       pdb=" N   PRO A 328 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.040 2.34e-02 1.83e+03 2.88e+00
  ... (remaining 7184 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 9455
        1.79 -     3.59: 249
        3.59 -     5.38: 29
        5.38 -     7.18: 12
        7.18 -     8.97: 10
  Bond angle restraints: 9755
  Sorted by residual:
  angle pdb=" C   LEU R 511 "
        pdb=" N   CYS R 512 "
        pdb=" CA  CYS R 512 "
      ideal   model   delta    sigma   weight residual
     121.70  129.94   -8.24 1.80e+00 3.09e-01 2.10e+01
  angle pdb=" CA  TRP R 482 "
        pdb=" CB  TRP R 482 "
        pdb=" CG  TRP R 482 "
      ideal   model   delta    sigma   weight residual
     113.60  106.81    6.79 1.90e+00 2.77e-01 1.28e+01
  angle pdb=" N   ARG R 223 "
        pdb=" CA  ARG R 223 "
        pdb=" CB  ARG R 223 "
      ideal   model   delta    sigma   weight residual
     110.12  115.22   -5.10 1.47e+00 4.63e-01 1.21e+01
  angle pdb=" C   PRO R 492 "
        pdb=" N   ILE R 493 "
        pdb=" CA  ILE R 493 "
      ideal   model   delta    sigma   weight residual
     120.62  125.57   -4.95 1.64e+00 3.72e-01 9.11e+00
  angle pdb=" N   VAL A 394 "
        pdb=" CA  VAL A 394 "
        pdb=" C   VAL A 394 "
      ideal   model   delta    sigma   weight residual
     111.00  102.65    8.35 2.80e+00 1.28e-01 8.88e+00
  ... (remaining 9750 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.19: 4176
       26.19 -    52.38: 113
       52.38 -    78.57: 8
       78.57 -   104.76: 2
      104.76 -   130.95: 1
  Dihedral angle restraints: 4300
    sinusoidal: 1690
      harmonic: 2610
  Sorted by residual:
  dihedral pdb=" C05 IXO R 601 "
           pdb=" C06 IXO R 601 "
           pdb=" C07 IXO R 601 "
           pdb=" C08 IXO R 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.37   50.42  130.95     1      3.00e+01 1.11e-03 1.77e+01
  dihedral pdb=" CA  PHE B 335 "
           pdb=" C   PHE B 335 "
           pdb=" N   LEU B 336 "
           pdb=" CA  LEU B 336 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.67   19.33     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  ASP B 254 "
           pdb=" CB  ASP B 254 "
           pdb=" CG  ASP B 254 "
           pdb=" OD1 ASP B 254 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.82   56.82     1      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 4297 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 849
       0.051 -    0.103: 218
       0.103 -    0.154: 47
       0.154 -    0.205: 9
       0.205 -    0.257: 2
  Chirality restraints: 1125
  Sorted by residual:
  chirality pdb=" CG  LEU R  70 "
            pdb=" CB  LEU R  70 "
            pdb=" CD1 LEU R  70 "
            pdb=" CD2 LEU R  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.85    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  VAL R 462 "
            pdb=" CA  VAL R 462 "
            pdb=" CG1 VAL R 462 "
            pdb=" CG2 VAL R 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  VAL A 394 "
            pdb=" N   VAL A 394 "
            pdb=" C   VAL A 394 "
            pdb=" CB  VAL A 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.72e-01
  ... (remaining 1122 not shown)

  Planarity restraints: 1228
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 501 "   -0.017 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" C   THR R 501 "    0.058 2.00e-02 2.50e+03
        pdb=" O   THR R 501 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   PHE R 502 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R 482 "    0.015 2.00e-02 2.50e+03   2.98e-02 8.89e+00
        pdb=" C   TRP R 482 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   TRP R 482 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LEU R 483 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 446 "   -0.014 2.00e-02 2.50e+03   2.83e-02 7.99e+00
        pdb=" C   ALA R 446 "    0.049 2.00e-02 2.50e+03
        pdb=" O   ALA R 446 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE R 447 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1225 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1788
        2.80 -     3.32: 6170
        3.32 -     3.85: 11894
        3.85 -     4.37: 13837
        4.37 -     4.90: 23934
  Nonbonded interactions: 57623
  Sorted by model distance:
  nonbonded pdb=" O   ALA R 450 "
            pdb=" OG1 THR R 454 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OD2 ASP R 110 "
            pdb=" OH  TYR R 485 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ILE R 452 "
            pdb=" OG1 THR R 456 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG  SER R 131 "
            pdb=" OH  TYR A 391 "
     model   vdw
     2.325 3.040
  ... (remaining 57618 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.42 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.940
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
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      :  0.004   0.055   7191  Z= 0.194
  Angle     :  0.730   8.970   9759  Z= 0.397
  Chirality :  0.049   0.257   1125
  Planarity :  0.007   0.092   1228
  Dihedral  : 12.041 130.955   2598
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.78 %
    Favored  : 99.09 %
  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: -1.89 (0.25), residues: 877
  helix: -1.84 (0.20), residues: 386
  sheet:  0.64 (0.43), residues: 152
  loop : -1.22 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.001   ARG R 139 
 TYR   0.029   0.002   TYR R  87 
 PHE   0.030   0.002   PHE R 187 
 TRP   0.028   0.002   TRP R 482 
 HIS   0.008   0.002   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7189)
  covalent geometry    : angle       0.72934 ( 9755)
  SS BOND              : bond        0.00656 (    2)
  SS BOND              : angle       1.30347 (    4)
  hydrogen bonds       : bond        0.19122 (  376)
  hydrogen bonds       : angle       7.51226 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   49 VAL cc_start: 0.8836 (t) cc_final: 0.8582 (m)
REVERT: R   56 LYS cc_start: 0.8890 (tptp) cc_final: 0.8357 (tppp)
REVERT: R  141 LYS cc_start: 0.8624 (mttt) cc_final: 0.8260 (mtmt)
REVERT: R  146 ARG cc_start: 0.7461 (mmt90) cc_final: 0.6651 (ttt-90)
REVERT: R  221 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7858 (mt-10)
REVERT: R  225 LYS cc_start: 0.7706 (tptp) cc_final: 0.7135 (tppt)
REVERT: R  229 ASP cc_start: 0.7882 (m-30) cc_final: 0.7405 (m-30)
REVERT: R  500 ARG cc_start: 0.8913 (mtt-85) cc_final: 0.8622 (mmt90)
REVERT: R  507 LYS cc_start: 0.8576 (mmtt) cc_final: 0.7999 (mmpt)
REVERT: B  226 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8693 (tm-30)
REVERT: B  247 ASP cc_start: 0.8088 (t0) cc_final: 0.7865 (t0)
REVERT: B  280 LYS cc_start: 0.8873 (tptp) cc_final: 0.8612 (mmmm)
REVERT: A   25 MET cc_start: 0.8423 (ttm) cc_final: 0.8034 (tmm)
REVERT: A  390 GLU cc_start: 0.8734 (tp30) cc_final: 0.8529 (tt0)
  outliers start: 1
  outliers final: 1
  residues processed: 121
  average time/residue: 0.6270
  time to fit residues: 79.1802
Evaluate side-chains
  75 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  453 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    8.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
R  60 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.094487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.063770 restraints weight = 45409.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 5.14
r_work: 0.2999 rms_B_bonded: 5.08 restraints_weight: 2.0000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7191  Z= 0.191
  Angle     :  0.578   5.973   9759  Z= 0.307
  Chirality :  0.042   0.136   1125
  Planarity :  0.004   0.049   1228
  Dihedral  :  4.787  75.946    983
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  7.96 %
    Favored  : 90.60 %
  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:  0.09 (0.27), residues: 877
  helix:  0.65 (0.24), residues: 393
  sheet:  0.21 (0.38), residues: 173
  loop : -0.65 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 280 
 TYR   0.015   0.002   TYR B  59 
 PHE   0.016   0.001   PHE R 187 
 TRP   0.021   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 7189)
  covalent geometry    : angle       0.57848 ( 9755)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.62325 (    4)
  hydrogen bonds       : bond        0.04481 (  376)
  hydrogen bonds       : angle       4.70335 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   56 LYS cc_start: 0.8965 (tptp) cc_final: 0.8438 (tppp)
REVERT: R  141 LYS cc_start: 0.8892 (mttt) cc_final: 0.8470 (mtmt)
REVERT: R  146 ARG cc_start: 0.7973 (mmt90) cc_final: 0.7199 (ttt-90)
REVERT: R  190 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7484 (mt-10)
REVERT: R  225 LYS cc_start: 0.8294 (tptp) cc_final: 0.7749 (tppt)
REVERT: R  229 ASP cc_start: 0.8172 (m-30) cc_final: 0.7747 (m-30)
REVERT: R  500 ARG cc_start: 0.8968 (mtt-85) cc_final: 0.8706 (mmt90)
REVERT: R  507 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8245 (mmpt)
REVERT: B  172 GLU cc_start: 0.9239 (tp30) cc_final: 0.8997 (tp30)
REVERT: B  226 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8676 (tm-30)
REVERT: B  247 ASP cc_start: 0.8291 (t0) cc_final: 0.8026 (t0)
REVERT: B  262 MET cc_start: 0.8781 (tpp) cc_final: 0.8574 (tpp)
REVERT: B  280 LYS cc_start: 0.8707 (tptp) cc_final: 0.8455 (mmmm)
REVERT: A   25 MET cc_start: 0.8389 (ttm) cc_final: 0.8080 (tmm)
REVERT: G   50 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6112 (mp)
  outliers start: 11
  outliers final: 2
  residues processed: 82
  average time/residue: 0.8060
  time to fit residues: 68.8113
Evaluate side-chains
  68 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  156 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain G residue   50 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
G  18 GLN
G  44 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.093863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.062465 restraints weight = 46570.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 5.37
r_work: 0.2953 rms_B_bonded: 5.20 restraints_weight: 2.0000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7191  Z= 0.137
  Angle     :  0.528   8.757   9759  Z= 0.278
  Chirality :  0.041   0.200   1125
  Planarity :  0.004   0.034   1228
  Dihedral  :  4.551  72.236    981
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.14 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.28), residues: 877
  helix:  1.47 (0.25), residues: 393
  sheet:  0.13 (0.38), residues: 173
  loop : -0.50 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 280 
 TYR   0.013   0.001   TYR B 264 
 PHE   0.014   0.001   PHE R 187 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7189)
  covalent geometry    : angle       0.52783 ( 9755)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       0.25125 (    4)
  hydrogen bonds       : bond        0.04093 (  376)
  hydrogen bonds       : angle       4.45167 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: R   56 LYS cc_start: 0.8960 (tptp) cc_final: 0.8418 (tppp)
REVERT: R  141 LYS cc_start: 0.8770 (mttt) cc_final: 0.8343 (mtmt)
REVERT: R  146 ARG cc_start: 0.7911 (mmt90) cc_final: 0.7091 (ttt-90)
REVERT: R  225 LYS cc_start: 0.8186 (tptp) cc_final: 0.7907 (tppt)
REVERT: R  229 ASP cc_start: 0.8168 (m-30) cc_final: 0.7940 (m-30)
REVERT: R  439 LYS cc_start: 0.8464 (tttm) cc_final: 0.8146 (tttm)
REVERT: R  500 ARG cc_start: 0.8967 (mtt-85) cc_final: 0.8758 (mmt90)
REVERT: R  507 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8258 (mmpt)
REVERT: B   23 LYS cc_start: 0.9540 (tppt) cc_final: 0.9197 (mttm)
REVERT: B  130 GLU cc_start: 0.8164 (pt0) cc_final: 0.7406 (pp20)
REVERT: B  215 GLU cc_start: 0.8216 (tt0) cc_final: 0.7802 (pp20)
REVERT: B  226 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8664 (tm-30)
REVERT: B  247 ASP cc_start: 0.8343 (t0) cc_final: 0.8046 (t0)
REVERT: B  262 MET cc_start: 0.8747 (tpp) cc_final: 0.8474 (tpp)
REVERT: B  277 SER cc_start: 0.9027 (t) cc_final: 0.8746 (p)
REVERT: B  301 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8428 (mmtt)
REVERT: A   25 MET cc_start: 0.8313 (ttm) cc_final: 0.8016 (tmm)
  outliers start: 11
  outliers final: 2
  residues processed: 74
  average time/residue: 0.7365
  time to fit residues: 56.9338
Evaluate side-chains
  64 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain G residue   54 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 74 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 83 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
G  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.094352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.063546 restraints weight = 35065.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 4.79
r_work: 0.2954 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7191  Z= 0.137
  Angle     :  0.529   8.756   9759  Z= 0.278
  Chirality :  0.041   0.198   1125
  Planarity :  0.003   0.034   1228
  Dihedral  :  4.742  72.226    981
  Min Nonbonded Distance : 1.693

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 11.49 %
    Favored  : 87.99 %
  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:  0.73 (0.28), residues: 877
  helix:  1.48 (0.25), residues: 393
  sheet:  0.13 (0.38), residues: 173
  loop : -0.50 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 223 
 TYR   0.013   0.001   TYR B 264 
 PHE   0.014   0.001   PHE R 187 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7189)
  covalent geometry    : angle       0.52954 ( 9755)
  SS BOND              : bond        0.00073 (    2)
  SS BOND              : angle       0.25215 (    4)
  hydrogen bonds       : bond        0.04091 (  376)
  hydrogen bonds       : angle       4.45174 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: R   56 LYS cc_start: 0.8959 (tptp) cc_final: 0.8416 (tppp)
REVERT: R  141 LYS cc_start: 0.8752 (mttt) cc_final: 0.8328 (mtmt)
REVERT: R  146 ARG cc_start: 0.7867 (mmt90) cc_final: 0.7045 (ttt-90)
REVERT: R  225 LYS cc_start: 0.8135 (tptp) cc_final: 0.7860 (tppt)
REVERT: R  229 ASP cc_start: 0.8115 (m-30) cc_final: 0.7881 (m-30)
REVERT: R  439 LYS cc_start: 0.8417 (tttm) cc_final: 0.8094 (tttm)
REVERT: R  500 ARG cc_start: 0.8970 (mtt-85) cc_final: 0.8756 (mmt90)
REVERT: R  507 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8255 (mmpt)
REVERT: B   23 LYS cc_start: 0.9544 (tppt) cc_final: 0.9207 (mttm)
REVERT: B  130 GLU cc_start: 0.8049 (pt0) cc_final: 0.7384 (pp20)
REVERT: B  226 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8668 (tm-30)
REVERT: B  247 ASP cc_start: 0.8347 (t0) cc_final: 0.8041 (t0)
REVERT: B  262 MET cc_start: 0.8602 (tpp) cc_final: 0.8398 (tpp)
REVERT: B  277 SER cc_start: 0.8951 (t) cc_final: 0.8632 (p)
REVERT: B  301 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8408 (mmtt)
REVERT: A   25 MET cc_start: 0.8281 (ttm) cc_final: 0.7991 (tmm)
  outliers start: 4
  outliers final: 3
  residues processed: 63
  average time/residue: 0.6668
  time to fit residues: 43.8165
Evaluate side-chains
  65 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain G residue   54 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 69 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 15 optimal weight:    8.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
R  85 ASN
B  88 ASN
G  18 GLN
G  44 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.092225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.060483 restraints weight = 44256.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 5.20
r_work: 0.2889 rms_B_bonded: 5.11 restraints_weight: 2.0000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7191  Z= 0.216
  Angle     :  0.573   8.466   9759  Z= 0.301
  Chirality :  0.043   0.165   1125
  Planarity :  0.004   0.040   1228
  Dihedral  :  4.626  68.398    981
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.05 %
    Favored  : 88.51 %
  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 (0.29), residues: 877
  helix:  1.89 (0.26), residues: 388
  sheet:  0.05 (0.37), residues: 178
  loop : -0.30 (0.39), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 214 
 TYR   0.019   0.002   TYR B 105 
 PHE   0.015   0.001   PHE R 187 
 TRP   0.019   0.002   TRP B 211 
 HIS   0.006   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 7189)
  covalent geometry    : angle       0.57279 ( 9755)
  SS BOND              : bond        0.00173 (    2)
  SS BOND              : angle       0.59221 (    4)
  hydrogen bonds       : bond        0.04247 (  376)
  hydrogen bonds       : angle       4.40869 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: R   56 LYS cc_start: 0.8986 (tptp) cc_final: 0.8437 (tppp)
REVERT: R  141 LYS cc_start: 0.8726 (mttt) cc_final: 0.8276 (mtpt)
REVERT: R  146 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7055 (ttt-90)
REVERT: R  190 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7408 (mt-10)
REVERT: R  500 ARG cc_start: 0.9008 (mtt-85) cc_final: 0.8675 (mmt90)
REVERT: R  507 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8319 (mmpt)
REVERT: B  130 GLU cc_start: 0.8040 (pt0) cc_final: 0.7359 (pp20)
REVERT: B  217 MET cc_start: 0.7710 (pp-130) cc_final: 0.7357 (pp-130)
REVERT: B  226 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8655 (tm-30)
REVERT: B  247 ASP cc_start: 0.8524 (t0) cc_final: 0.8167 (t0)
REVERT: B  280 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8393 (tttp)
REVERT: B  301 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8455 (mmtt)
REVERT: A   25 MET cc_start: 0.8301 (ttm) cc_final: 0.7996 (tmm)
  outliers start: 11
  outliers final: 7
  residues processed: 72
  average time/residue: 0.7233
  time to fit residues: 54.1739
Evaluate side-chains
  70 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   28 TRP
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  229 ASP
Chi-restraints excluded: chain R residue  453 ILE
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   47 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0980
   chunk 74 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0070
   chunk 18 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.092093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.060592 restraints weight = 42533.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 5.07
r_work: 0.2890 rms_B_bonded: 5.06 restraints_weight: 2.0000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7191  Z= 0.214
  Angle     :  0.572   8.465   9759  Z= 0.301
  Chirality :  0.043   0.164   1125
  Planarity :  0.004   0.040   1228
  Dihedral  :  4.957  68.391    981
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.01 %
    Favored  : 87.08 %
  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:  1.08 (0.29), residues: 877
  helix:  1.90 (0.26), residues: 388
  sheet:  0.05 (0.37), residues: 178
  loop : -0.30 (0.39), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 214 
 TYR   0.018   0.002   TYR B 105 
 PHE   0.015   0.001   PHE R 187 
 TRP   0.018   0.002   TRP B 211 
 HIS   0.006   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 ( 7189)
  covalent geometry    : angle       0.57221 ( 9755)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.59206 (    4)
  hydrogen bonds       : bond        0.04242 (  376)
  hydrogen bonds       : angle       4.40873 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: R   56 LYS cc_start: 0.8987 (tptp) cc_final: 0.8439 (tppp)
REVERT: R  141 LYS cc_start: 0.8737 (mttt) cc_final: 0.8296 (mtpt)
REVERT: R  146 ARG cc_start: 0.7880 (mmt90) cc_final: 0.7060 (ttt-90)
REVERT: R  190 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7433 (mt-10)
REVERT: R  500 ARG cc_start: 0.8999 (mtt-85) cc_final: 0.8684 (mmt90)
REVERT: R  507 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8328 (mmpt)
REVERT: B  130 GLU cc_start: 0.8022 (pt0) cc_final: 0.7333 (pp20)
REVERT: B  226 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8648 (tm-30)
REVERT: B  247 ASP cc_start: 0.8499 (t0) cc_final: 0.8140 (t0)
REVERT: B  280 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8406 (tttp)
REVERT: B  301 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8457 (mmtt)
REVERT: A   25 MET cc_start: 0.8308 (ttm) cc_final: 0.8005 (tmm)
  outliers start: 7
  outliers final: 7
  residues processed: 65
  average time/residue: 0.7874
  time to fit residues: 53.2712
Evaluate side-chains
  70 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   28 TRP
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  229 ASP
Chi-restraints excluded: chain R residue  453 ILE
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   47 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 75 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.092652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.063443 restraints weight = 32037.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 5.02
r_work: 0.2905 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2912
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2912
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7191  Z= 0.166
  Angle     :  0.570  10.342   9759  Z= 0.296
  Chirality :  0.042   0.145   1125
  Planarity :  0.004   0.038   1228
  Dihedral  :  4.250  45.525    981
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.75 %
    Favored  : 87.47 %
  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:  1.21 (0.29), residues: 877
  helix:  2.06 (0.26), residues: 387
  sheet:  0.09 (0.37), residues: 171
  loop : -0.28 (0.39), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 129 
 TYR   0.014   0.001   TYR B 264 
 PHE   0.013   0.001   PHE R 187 
 TRP   0.017   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 7189)
  covalent geometry    : angle       0.56957 ( 9755)
  SS BOND              : bond        0.00104 (    2)
  SS BOND              : angle       0.52809 (    4)
  hydrogen bonds       : bond        0.04079 (  376)
  hydrogen bonds       : angle       4.36510 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   50 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8158 (mp)
REVERT: R   56 LYS cc_start: 0.8978 (tptp) cc_final: 0.8420 (tppp)
REVERT: R  141 LYS cc_start: 0.8705 (mttt) cc_final: 0.8244 (mtpt)
REVERT: R  146 ARG cc_start: 0.7839 (mmt90) cc_final: 0.7001 (ttt-90)
REVERT: R  190 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7352 (mt-10)
REVERT: R  500 ARG cc_start: 0.9018 (mtt-85) cc_final: 0.8685 (mmt90)
REVERT: R  507 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8302 (mmpt)
REVERT: B  226 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8786 (mm-30)
REVERT: B  247 ASP cc_start: 0.8518 (t0) cc_final: 0.8205 (t0)
REVERT: B  280 LYS cc_start: 0.8800 (tmtm) cc_final: 0.8418 (tttp)
REVERT: B  301 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8465 (mmtt)
REVERT: A   25 MET cc_start: 0.8292 (ttm) cc_final: 0.7986 (tmm)
  outliers start: 6
  outliers final: 5
  residues processed: 66
  average time/residue: 0.7670
  time to fit residues: 52.8431
Evaluate side-chains
  67 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   28 TRP
Chi-restraints excluded: chain R residue   50 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  453 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   47 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 84 optimal weight:   20.0000
   chunk 16 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0980
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0170
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.8020

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.092782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.061585 restraints weight = 38402.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 4.88
r_work: 0.2907 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7191  Z= 0.166
  Angle     :  0.570  10.342   9759  Z= 0.296
  Chirality :  0.042   0.145   1125
  Planarity :  0.004   0.038   1228
  Dihedral  :  4.250  45.525    981
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.14 %
    Favored  : 86.95 %
  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:  1.21 (0.29), residues: 877
  helix:  2.06 (0.26), residues: 387
  sheet:  0.09 (0.37), residues: 171
  loop : -0.28 (0.39), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 129 
 TYR   0.014   0.001   TYR B 264 
 PHE   0.013   0.001   PHE R 187 
 TRP   0.017   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 7189)
  covalent geometry    : angle       0.56957 ( 9755)
  SS BOND              : bond        0.00104 (    2)
  SS BOND              : angle       0.52809 (    4)
  hydrogen bonds       : bond        0.04079 (  376)
  hydrogen bonds       : angle       4.36510 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   50 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8218 (mp)
REVERT: R   56 LYS cc_start: 0.8988 (tptp) cc_final: 0.8434 (tppp)
REVERT: R  141 LYS cc_start: 0.8755 (mttt) cc_final: 0.8304 (mtpt)
REVERT: R  146 ARG cc_start: 0.7883 (mmt90) cc_final: 0.7049 (ttt-90)
REVERT: R  190 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7415 (mt-10)
REVERT: R  500 ARG cc_start: 0.8986 (mtt-85) cc_final: 0.8687 (mmt90)
REVERT: R  507 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8322 (mmpt)
REVERT: B  226 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8785 (mm-30)
REVERT: B  247 ASP cc_start: 0.8505 (t0) cc_final: 0.8196 (t0)
REVERT: B  280 LYS cc_start: 0.8829 (tmtm) cc_final: 0.8451 (tttp)
REVERT: B  301 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8484 (mmtt)
REVERT: A   25 MET cc_start: 0.8312 (ttm) cc_final: 0.8020 (tmm)
  outliers start: 7
  outliers final: 5
  residues processed: 64
  average time/residue: 0.8360
  time to fit residues: 55.7242
Evaluate side-chains
  67 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   28 TRP
Chi-restraints excluded: chain R residue   50 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  453 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   47 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 86 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0670
   chunk 68 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 84 optimal weight:    0.0980
   chunk 50 optimal weight:    7.9990
   chunk 76 optimal weight:    7.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.5320

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.093832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.063204 restraints weight = 32503.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 4.56
r_work: 0.2965 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2969
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2969 r_free = 0.2969    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2969
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7191  Z= 0.115
  Angle     :  0.560  10.091   9759  Z= 0.289
  Chirality :  0.041   0.137   1125
  Planarity :  0.003   0.040   1228
  Dihedral  :  4.075  35.471    981
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.14 %
    Favored  : 87.21 %
  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:  1.33 (0.29), residues: 877
  helix:  2.23 (0.26), residues: 387
  sheet:  0.05 (0.37), residues: 171
  loop : -0.26 (0.39), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 129 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.011   0.001   PHE R 187 
 TRP   0.020   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7189)
  covalent geometry    : angle       0.55986 ( 9755)
  SS BOND              : bond        0.00112 (    2)
  SS BOND              : angle       0.62609 (    4)
  hydrogen bonds       : bond        0.03709 (  376)
  hydrogen bonds       : angle       4.21377 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: R   50 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8199 (mp)
REVERT: R   56 LYS cc_start: 0.8980 (tptp) cc_final: 0.8424 (tppp)
REVERT: R  141 LYS cc_start: 0.8737 (mttt) cc_final: 0.8275 (mtpt)
REVERT: R  146 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7032 (ttt-90)
REVERT: R  190 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7387 (mt-10)
REVERT: R  439 LYS cc_start: 0.8543 (tttm) cc_final: 0.8254 (tttm)
REVERT: R  500 ARG cc_start: 0.8970 (mtt-85) cc_final: 0.8715 (mmt90)
REVERT: R  507 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8414 (mptt)
REVERT: B   23 LYS cc_start: 0.9489 (tppt) cc_final: 0.9127 (mttp)
REVERT: B  226 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8646 (tm-30)
REVERT: B  247 ASP cc_start: 0.8484 (t0) cc_final: 0.8133 (t0)
REVERT: B  277 SER cc_start: 0.8974 (t) cc_final: 0.8672 (p)
REVERT: B  280 LYS cc_start: 0.8788 (tmtm) cc_final: 0.8538 (tttp)
REVERT: B  301 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8444 (mmtt)
REVERT: A   25 MET cc_start: 0.8265 (ttm) cc_final: 0.7995 (tmm)
  outliers start: 5
  outliers final: 3
  residues processed: 68
  average time/residue: 0.8272
  time to fit residues: 58.5903
Evaluate side-chains
  67 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   28 TRP
Chi-restraints excluded: chain R residue   50 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  453 ILE
Chi-restraints excluded: chain G residue   38 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R  60 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.093532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.062007 restraints weight = 44780.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 5.24
r_work: 0.2948 rms_B_bonded: 5.15 restraints_weight: 2.0000
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2953
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7191  Z= 0.117
  Angle     :  0.534   9.046   9759  Z= 0.278
  Chirality :  0.041   0.133   1125
  Planarity :  0.003   0.031   1228
  Dihedral  :  3.970  33.038    981
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.01 %
    Favored  : 87.34 %
  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:  1.37 (0.29), residues: 877
  helix:  2.31 (0.26), residues: 387
  sheet:  0.04 (0.37), residues: 171
  loop : -0.29 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 214 
 TYR   0.009   0.001   TYR R 495 
 PHE   0.011   0.001   PHE R 187 
 TRP   0.018   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7189)
  covalent geometry    : angle       0.53381 ( 9755)
  SS BOND              : bond        0.00071 (    2)
  SS BOND              : angle       0.60205 (    4)
  hydrogen bonds       : bond        0.03641 (  376)
  hydrogen bonds       : angle       4.16866 ( 1098)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   50 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8240 (mp)
REVERT: R   56 LYS cc_start: 0.8985 (tptp) cc_final: 0.8426 (tppp)
REVERT: R  141 LYS cc_start: 0.8798 (mttt) cc_final: 0.8341 (mtpt)
REVERT: R  146 ARG cc_start: 0.7919 (mmt90) cc_final: 0.7090 (ttt-90)
REVERT: R  190 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7421 (mt-10)
REVERT: R  221 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8060 (mt-10)
REVERT: R  439 LYS cc_start: 0.8572 (tttm) cc_final: 0.8289 (tttm)
REVERT: R  500 ARG cc_start: 0.8978 (mtt-85) cc_final: 0.8731 (mmt90)
REVERT: R  507 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8410 (mptt)
REVERT: B  226 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8634 (tm-30)
REVERT: B  247 ASP cc_start: 0.8493 (t0) cc_final: 0.8158 (t0)
REVERT: B  277 SER cc_start: 0.9047 (t) cc_final: 0.8791 (p)
REVERT: B  280 LYS cc_start: 0.8831 (tmtm) cc_final: 0.8590 (tttp)
REVERT: A   25 MET cc_start: 0.8315 (ttm) cc_final: 0.8038 (tmm)
  outliers start: 5
  outliers final: 4
  residues processed: 65
  average time/residue: 0.8113
  time to fit residues: 55.0379
Evaluate side-chains
  64 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   28 TRP
Chi-restraints excluded: chain R residue   50 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  453 ILE
Chi-restraints excluded: chain G residue   38 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 62 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0670
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
R  60 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.093724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.064747 restraints weight = 31947.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 4.90
r_work: 0.2935 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7191  Z= 0.117
  Angle     :  0.534   9.046   9759  Z= 0.278
  Chirality :  0.041   0.133   1125
  Planarity :  0.003   0.031   1228
  Dihedral  :  3.971  33.038    981
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.01 %
    Favored  : 87.08 %
  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:  1.37 (0.29), residues: 877
  helix:  2.31 (0.26), residues: 387
  sheet:  0.04 (0.37), residues: 171
  loop : -0.29 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 214 
 TYR   0.009   0.001   TYR R 495 
 PHE   0.011   0.001   PHE R 187 
 TRP   0.018   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7189)
  covalent geometry    : angle       0.53381 ( 9755)
  SS BOND              : bond        0.00071 (    2)
  SS BOND              : angle       0.60205 (    4)
  hydrogen bonds       : bond        0.03641 (  376)
  hydrogen bonds       : angle       4.16866 ( 1098)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3182.21 seconds
wall clock time: 54 minutes 58.23 seconds (3298.23 seconds total)