Starting phenix.real_space_refine
on Wed Sep 17 15:05:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8csx_26974/09_2025/8csx_26974.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8csx_26974/09_2025/8csx_26974.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8csx_26974/09_2025/8csx_26974.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8csx_26974/09_2025/8csx_26974.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8csx_26974/09_2025/8csx_26974.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8csx_26974/09_2025/8csx_26974.map"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.322
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      66      5.16       5
     C    5941      2.51       5
     N    1424      2.21       5
     O    1685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9116
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "K"
      Number of atoms: 2943
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 380, 2919
          Classifications: {'peptide': 380}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 14, 'TRANS': 365}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
      Conformer: "B"
        Number of residues, atoms: 380, 2919
          Classifications: {'peptide': 380}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 14, 'TRANS': 365}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
          bond proxies already assigned to first conformer: 2962
    Chain: "L"
      Number of atoms: 2938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 2938
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 376}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "Q"
      Number of atoms: 2954
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 2954
          Classifications: {'peptide': 390}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 378}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "Q"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 75
          Unusual residues: {'AJP': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 224
          Unresolved non-hydrogen chiralities: 43
    Chain: "K"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 32
          Classifications: {'water': 32}
          Link IDs: {None: 31}
    Chain: "L"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 67
          Classifications: {'water': 67}
          Link IDs: {None: 66}
    Chain: "Q"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 51
          Classifications: {'water': 51}
          Link IDs: {None: 50}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ATYR K  34 " occ=0.55
      ... (22 atoms not shown)
      pdb=" OH BTYR K  34 " occ=0.45
    residue:
      pdb=" N  ATYR K 242 " occ=0.53
      ... (22 atoms not shown)
      pdb=" OH BTYR K 242 " occ=0.47
  Time building chain proxies: 2.96, per 1000 atoms: 0.32
  Number of scatterers: 9116
  At special positions: 0
  Unit cell: (91.3, 89.64, 92.13, 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      66     16.00
     O    1685      8.00
     N    1424      7.00
     C    5941      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 324.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 3 sheets defined
      79.2% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'K' and resid 11 through 31
    Processing helix  chain 'K' and resid 43 through 60
      removed outlier: 3.889A  pdb=" N   VAL K  50 " --> pdb=" O   ALA K  46 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY K  51 " --> pdb=" O   SER K  47 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 60 through 66
      removed outlier: 3.872A  pdb=" N   THR K  66 " --> pdb=" O   LEU K  62 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 72 through 99
      removed outlier: 3.647A  pdb=" N   GLN K  89 " --> pdb=" O   ALA K  85 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU K  93 " --> pdb=" O   GLN K  89 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 109 through 128
      removed outlier: 3.592A  pdb=" N   VAL K 123 " --> pdb=" O   SER K 119 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY K 128 " --> pdb=" O   LEU K 124 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 135 through 162
    Processing helix  chain 'K' and resid 166 through 170
      removed outlier: 3.562A  pdb=" N   LEU K 169 " --> pdb=" O   HIS K 166 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG K 170 " --> pdb=" O   MET K 167 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 166 through 170'
    Processing helix  chain 'K' and resid 171 through 187
      removed outlier: 3.569A  pdb=" N   CYS K 186 " --> pdb=" O   THR K 182 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU K 187 " --> pdb=" O   VAL K 183 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 202 through 225
      Proline residue:  K 221  - end of helix
    Processing helix  chain 'K' and resid 230 through 256
    Processing helix  chain 'K' and resid 266 through 274
      removed outlier: 3.628A  pdb=" N   SER K 272 " --> pdb=" O   THR K 268 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 275 through 282
    Processing helix  chain 'K' and resid 290 through 312
      removed outlier: 3.701A  pdb=" N   ALA K 294 " --> pdb=" O   SER K 290 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 326 through 350
      removed outlier: 3.602A  pdb=" N   VAL K 348 " --> pdb=" O   ILE K 344 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU K 349 " --> pdb=" O   VAL K 345 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 361 through 389
    Processing helix  chain 'K' and resid 390 through 394
    Processing helix  chain 'K' and resid 397 through 401
      removed outlier: 3.714A  pdb=" N   TYR K 401 " --> pdb=" O   VAL K 398 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 403 through 407
    Processing helix  chain 'L' and resid 3 through 23
    Processing helix  chain 'L' and resid 50 through 63
    Processing helix  chain 'L' and resid 63 through 69
    Processing helix  chain 'L' and resid 75 through 104
      removed outlier: 3.739A  pdb=" N   GLN L  92 " --> pdb=" O   ALA L  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 111 through 133
      removed outlier: 3.711A  pdb=" N   ALA L 131 " --> pdb=" O   ILE L 127 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   VAL L 132 " --> pdb=" O   SER L 128 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 137 through 162
      removed outlier: 3.639A  pdb=" N   VAL L 150 " --> pdb=" O   ILE L 146 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 174 through 189
    Processing helix  chain 'L' and resid 191 through 195
    Processing helix  chain 'L' and resid 204 through 228
      removed outlier: 3.743A  pdb=" N   ILE L 213 " --> pdb=" O   LEU L 209 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY L 214 " --> pdb=" O   PHE L 210 " (cutoff:3.500A)
      Proline residue:  L 223  - end of helix
    Processing helix  chain 'L' and resid 233 through 261
      removed outlier: 3.714A  pdb=" N   LEU L 252 " --> pdb=" O   ALA L 248 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 262 through 266
    Processing helix  chain 'L' and resid 268 through 275
    Processing helix  chain 'L' and resid 277 through 283
      removed outlier: 3.657A  pdb=" N   VAL L 281 " --> pdb=" O   LEU L 277 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 291 through 321
      removed outlier: 4.546A  pdb=" N   THR L 315 " --> pdb=" O   TYR L 311 " (cutoff:3.500A)
      Proline residue:  L 316  - end of helix
    Processing helix  chain 'L' and resid 329 through 334
    Processing helix  chain 'L' and resid 334 through 351
    Processing helix  chain 'L' and resid 357 through 384
    Processing helix  chain 'L' and resid 398 through 402
      removed outlier: 3.619A  pdb=" N   VAL L 401 " --> pdb=" O   ASP L 398 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 3 through 23
    Processing helix  chain 'Q' and resid 47 through 63
      Proline residue:  Q  52  - end of helix
    Processing helix  chain 'Q' and resid 63 through 69
      removed outlier: 3.621A  pdb=" N   MET Q  69 " --> pdb=" O   PHE Q  65 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 70 through 72
      No H-bonds generated for 'chain 'Q' and resid 70 through 72'
    Processing helix  chain 'Q' and resid 75 through 104
      removed outlier: 3.812A  pdb=" N   GLN Q  92 " --> pdb=" O   ALA Q  88 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 111 through 133
      removed outlier: 3.507A  pdb=" N   MET Q 115 " --> pdb=" O   GLY Q 111 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA Q 131 " --> pdb=" O   ILE Q 127 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL Q 132 " --> pdb=" O   SER Q 128 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 137 through 162
      removed outlier: 3.688A  pdb=" N   VAL Q 150 " --> pdb=" O   ILE Q 146 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 174 through 189
    Processing helix  chain 'Q' and resid 191 through 195
    Processing helix  chain 'Q' and resid 204 through 228
      Proline residue:  Q 223  - end of helix
    Processing helix  chain 'Q' and resid 233 through 262
      removed outlier: 3.716A  pdb=" N   LEU Q 252 " --> pdb=" O   ALA Q 248 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 263 through 266
    Processing helix  chain 'Q' and resid 268 through 275
    Processing helix  chain 'Q' and resid 277 through 283
    Processing helix  chain 'Q' and resid 292 through 321
      removed outlier: 4.513A  pdb=" N   THR Q 315 " --> pdb=" O   TYR Q 311 " (cutoff:3.500A)
      Proline residue:  Q 316  - end of helix
    Processing helix  chain 'Q' and resid 329 through 334
    Processing helix  chain 'Q' and resid 335 through 351
    Processing helix  chain 'Q' and resid 357 through 385
      removed outlier: 4.028A  pdb=" N   LEU Q 385 " --> pdb=" O   LEU Q 381 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 398 through 402
      removed outlier: 3.583A  pdb=" N   VAL Q 401 " --> pdb=" O   ASP Q 398 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 32 through 34
      removed outlier: 6.923A  pdb=" N   HIS K  33 " --> pdb=" O   ILE K 108 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 25
    Processing sheet with id=AA3, first strand: chain 'Q' and resid 24 through 25

    658 hydrogen bonds defined for protein.
    1933 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.51

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1413
        1.32 -     1.44: 2492
        1.44 -     1.57: 5177
        1.57 -     1.69: 0
        1.69 -     1.81: 117
  Bond restraints: 9199
  Sorted by residual:
  bond pdb=" C   PRO Q 293 "
       pdb=" O   PRO Q 293 "
    ideal  model  delta    sigma   weight residual
    1.237  1.197  0.040 1.26e-02 6.30e+03 1.01e+01
  bond pdb=" N   VAL Q 373 "
       pdb=" CA  VAL Q 373 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.02e+00
  bond pdb=" N   TYR Q 180 "
       pdb=" CA  TYR Q 180 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.21e-02 6.83e+03 7.97e+00
  bond pdb=" N   LEU Q 383 "
       pdb=" CA  LEU Q 383 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.036 1.28e-02 6.10e+03 7.70e+00
  bond pdb=" N   ILE Q 188 "
       pdb=" CA  ILE Q 188 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.032 1.19e-02 7.06e+03 7.13e+00
  ... (remaining 9194 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 12044
        1.85 -     3.70: 417
        3.70 -     5.56: 51
        5.56 -     7.41: 12
        7.41 -     9.26: 4
  Bond angle restraints: 12528
  Sorted by residual:
  angle pdb=" N   LEU Q 189 "
        pdb=" CA  LEU Q 189 "
        pdb=" C   LEU Q 189 "
      ideal   model   delta    sigma   weight residual
     113.02  107.62    5.40 1.20e+00 6.94e-01 2.03e+01
  angle pdb=" N   ALA Q 353 "
        pdb=" CA  ALA Q 353 "
        pdb=" C   ALA Q 353 "
      ideal   model   delta    sigma   weight residual
     111.28  106.39    4.89 1.09e+00 8.42e-01 2.01e+01
  angle pdb=" C   ARG Q 323 "
        pdb=" N   ILE Q 324 "
        pdb=" CA  ILE Q 324 "
      ideal   model   delta    sigma   weight residual
     123.12  117.34    5.78 1.30e+00 5.92e-01 1.98e+01
  angle pdb=" CA  TYR Q 180 "
        pdb=" C   TYR Q 180 "
        pdb=" O   TYR Q 180 "
      ideal   model   delta    sigma   weight residual
     120.55  116.12    4.43 1.06e+00 8.90e-01 1.75e+01
  angle pdb=" C   TYR Q 180 "
        pdb=" CA  TYR Q 180 "
        pdb=" CB  TYR Q 180 "
      ideal   model   delta    sigma   weight residual
     110.79  117.41   -6.62 1.66e+00 3.63e-01 1.59e+01
  ... (remaining 12523 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.86: 5362
       30.86 -    61.72: 152
       61.72 -    92.58: 20
       92.58 -   123.44: 8
      123.44 -   154.30: 2
  Dihedral angle restraints: 5544
    sinusoidal: 2250
      harmonic: 3294
  Sorted by residual:
  dihedral pdb=" C   TYR Q 180 "
           pdb=" N   TYR Q 180 "
           pdb=" CA  TYR Q 180 "
           pdb=" CB  TYR Q 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.06   11.46     0      2.50e+00 1.60e-01 2.10e+01
  dihedral pdb=" C29 AJP Q 502 "
           pdb=" C30 AJP Q 502 "
           pdb=" C32 AJP Q 502 "
           pdb=" O33 AJP Q 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     299.04  144.74  154.30     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" O31 AJP Q 502 "
           pdb=" C30 AJP Q 502 "
           pdb=" C32 AJP Q 502 "
           pdb=" O33 AJP Q 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.28   23.48  153.80     1      3.00e+01 1.11e-03 2.02e+01
  ... (remaining 5541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1263
       0.067 -    0.134: 197
       0.134 -    0.202: 22
       0.202 -    0.269: 7
       0.269 -    0.336: 2
  Chirality restraints: 1491
  Sorted by residual:
  chirality pdb=" CA  TYR Q 180 "
            pdb=" N   TYR Q 180 "
            pdb=" C   TYR Q 180 "
            pdb=" CB  TYR Q 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" C11 AJP Q 501 "
            pdb=" C10 AJP Q 501 "
            pdb=" C12 AJP Q 501 "
            pdb=" C16 AJP Q 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.49   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" C08 AJP Q 502 "
            pdb=" C07 AJP Q 502 "
            pdb=" C10 AJP Q 502 "
            pdb=" O09 AJP Q 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.82   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1488 not shown)

  Planarity restraints: 1505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS Q 384 "    0.013 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   LYS Q 384 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   LYS Q 384 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU Q 385 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE Q 324 "   -0.012 2.00e-02 2.50e+03   2.45e-02 5.98e+00
        pdb=" C   ILE Q 324 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ILE Q 324 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   HIS Q 325 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY Q 345 "   -0.011 2.00e-02 2.50e+03   2.21e-02 4.88e+00
        pdb=" C   GLY Q 345 "    0.038 2.00e-02 2.50e+03
        pdb=" O   GLY Q 345 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE Q 346 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1502 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1044
        2.75 -     3.28: 9611
        3.28 -     3.82: 17718
        3.82 -     4.36: 21251
        4.36 -     4.90: 35084
  Nonbonded interactions: 84708
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP Q 399 "
            pdb=" O   HOH Q 601 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OD1 ASP Q 398 "
            pdb=" OG  SER Q 400 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   TYR K 178 "
            pdb=" OG1 THR K 182 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG1 THR L 408 "
            pdb=" O   HOH L 601 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   LYS L 404 "
            pdb=" O   HOH L 602 "
     model   vdw
     2.266 3.040
  ... (remaining 84703 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'L' and resid 1 through 409)
  selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409))
}

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=0.45 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.280
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
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      :  0.006   0.049   9199  Z= 0.307
  Angle     :  0.787   9.260  12528  Z= 0.483
  Chirality :  0.053   0.336   1491
  Planarity :  0.006   0.055   1505
  Dihedral  : 15.459 154.298   3440
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.67 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  :  5.58 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.10 %
  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 aren not related in a simple way.
  whole:  1.76 (0.24), residues: 1143
  helix:  1.68 (0.17), residues: 815
  sheet:  None (None), residues: 0
  loop : -0.01 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 191 
 TYR   0.027   0.003   TYR Q 180 
 PHE   0.021   0.003   PHE L  54 
 TRP   0.012   0.002   TRP K  16 
 HIS   0.006   0.002   HIS Q 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 9199)
  covalent geometry    : angle       0.78690 (12528)
  hydrogen bonds       : bond        0.12699 (  658)
  hydrogen bonds       : angle       5.93847 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 214
  time to evaluate  : 0.273 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6807 (mtm-85)
REVERT: K   16 TRP cc_start: 0.7806 (OUTLIER) cc_final: 0.5828 (t-100)
REVERT: K  100 GLN cc_start: 0.5257 (OUTLIER) cc_final: 0.4697 (tp-100)
REVERT: K  201 ARG cc_start: 0.8316 (mmt180) cc_final: 0.7921 (tpp-160)
REVERT: K  329 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.6212 (m-70)
REVERT: K  364 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6714 (mm)
REVERT: K  382 LEU cc_start: 0.8329 (mt) cc_final: 0.7832 (tp)
REVERT: K  390 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7760 (mp)
REVERT: L    2 ARG cc_start: 0.7458 (ptt90) cc_final: 0.7235 (ptt180)
REVERT: L  199 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6711 (pm20)
REVERT: L  202 GLU cc_start: 0.7898 (tt0) cc_final: 0.7632 (tt0)
REVERT: L  305 MET cc_start: 0.8291 (ttm) cc_final: 0.8054 (ttp)
REVERT: Q  196 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7370 (mmtt)
REVERT: Q  231 GLU cc_start: 0.7068 (tp30) cc_final: 0.6561 (tp30)
  outliers start: 36
  outliers final: 9
  residues processed: 233
  average time/residue: 0.5504
  time to fit residues: 136.8617
Evaluate side-chains
  198 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 182
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue   16 TRP
Chi-restraints excluded: chain K residue  100 GLN
Chi-restraints excluded: chain K residue  189 LYS
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  327 VAL
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  390 LEU
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  199 GLU
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  302 ILE
Chi-restraints excluded: chain Q residue  321 LYS
Chi-restraints excluded: chain Q residue  384 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
K  41 GLN
K  49 GLN
K 260 HIS
L  58 HIS
L 263 HIS
Q  55 GLN
Q 106 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.114202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.095018 restraints weight = 16409.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 1.27
r_work: 0.2815 rms_B_bonded: 1.70 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2700
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.0897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9199  Z= 0.208
  Angle     :  0.636   8.107  12528  Z= 0.340
  Chirality :  0.044   0.150   1491
  Planarity :  0.005   0.054   1505
  Dihedral  : 10.492 174.440   1602
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.76 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 10.30 %
    Favored  : 85.84 %
  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 aren not related in a simple way.
  whole:  1.99 (0.24), residues: 1143
  helix:  1.92 (0.17), residues: 806
  sheet:  None (None), residues: 0
  loop : -0.09 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q 238 
 TYR   0.022   0.003   TYR Q 244 
 PHE   0.022   0.002   PHE L  54 
 TRP   0.011   0.002   TRP K  16 
 HIS   0.005   0.001   HIS Q 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 9199)
  covalent geometry    : angle       0.63606 (12528)
  hydrogen bonds       : bond        0.06722 (  658)
  hydrogen bonds       : angle       5.22916 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 183
  time to evaluate  : 0.252 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7017 (mtt90)
REVERT: K  100 GLN cc_start: 0.5543 (OUTLIER) cc_final: 0.4887 (tp-100)
REVERT: K  201 ARG cc_start: 0.8288 (mmt180) cc_final: 0.7906 (tpp-160)
REVERT: K  329 HIS cc_start: 0.6372 (OUTLIER) cc_final: 0.5919 (m-70)
REVERT: K  382 LEU cc_start: 0.8294 (mt) cc_final: 0.7848 (tp)
REVERT: L  199 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7096 (pm20)
REVERT: L  202 GLU cc_start: 0.8269 (tt0) cc_final: 0.8046 (tt0)
REVERT: L  305 MET cc_start: 0.8399 (ttm) cc_final: 0.8174 (ttp)
REVERT: Q  196 LYS cc_start: 0.7854 (mmmm) cc_final: 0.7529 (mppt)
REVERT: Q  199 GLU cc_start: 0.7700 (pt0) cc_final: 0.7340 (pp20)
REVERT: Q  231 GLU cc_start: 0.7197 (tp30) cc_final: 0.6659 (tp30)
REVERT: Q  321 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7840 (mppt)
REVERT: Q  323 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8003 (mtt-85)
REVERT: Q  407 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7933 (tptp)
  outliers start: 36
  outliers final: 15
  residues processed: 200
  average time/residue: 0.5419
  time to fit residues: 115.5283
Evaluate side-chains
  208 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 186
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue   16 TRP
Chi-restraints excluded: chain K residue  100 GLN
Chi-restraints excluded: chain K residue  189 LYS
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  290 SER
Chi-restraints excluded: chain K residue  327 VAL
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  334 LEU
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  391 LYS
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  199 GLU
Chi-restraints excluded: chain Q residue   10 ILE
Chi-restraints excluded: chain Q residue  100 ILE
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  321 LYS
Chi-restraints excluded: chain Q residue  323 ARG
Chi-restraints excluded: chain Q residue  357 SER
Chi-restraints excluded: chain Q residue  377 LEU
Chi-restraints excluded: chain Q residue  407 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 103 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** K  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.114231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.094929 restraints weight = 16138.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 1.30
r_work: 0.2825 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9199  Z= 0.195
  Angle     :  0.617   7.839  12528  Z= 0.330
  Chirality :  0.043   0.162   1491
  Planarity :  0.005   0.041   1505
  Dihedral  :  9.483 143.196   1592
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 11.48 %
    Favored  : 84.55 %
  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 aren not related in a simple way.
  whole:  2.04 (0.24), residues: 1143
  helix:  1.98 (0.17), residues: 808
  sheet:  None (None), residues: 0
  loop : -0.13 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 154 
 TYR   0.022   0.003   TYR Q 244 
 PHE   0.021   0.002   PHE L  54 
 TRP   0.010   0.002   TRP K  16 
 HIS   0.005   0.001   HIS Q 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 9199)
  covalent geometry    : angle       0.61696 (12528)
  hydrogen bonds       : bond        0.06525 (  658)
  hydrogen bonds       : angle       5.15994 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 189
  time to evaluate  : 0.263 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7045 (mtt90)
REVERT: K  100 GLN cc_start: 0.5545 (OUTLIER) cc_final: 0.4976 (tp-100)
REVERT: K  201 ARG cc_start: 0.8262 (mmt180) cc_final: 0.7912 (tpp-160)
REVERT: K  329 HIS cc_start: 0.6334 (OUTLIER) cc_final: 0.5862 (m-70)
REVERT: K  364 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6689 (mm)
REVERT: K  382 LEU cc_start: 0.8290 (mt) cc_final: 0.7838 (tp)
REVERT: K  390 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7589 (mp)
REVERT: L  199 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7044 (pm20)
REVERT: L  202 GLU cc_start: 0.8245 (tt0) cc_final: 0.8013 (tt0)
REVERT: L  305 MET cc_start: 0.8379 (ttm) cc_final: 0.8150 (ttp)
REVERT: Q  196 LYS cc_start: 0.7848 (mmmm) cc_final: 0.7521 (mppt)
REVERT: Q  199 GLU cc_start: 0.7662 (pt0) cc_final: 0.7325 (pp20)
REVERT: Q  231 GLU cc_start: 0.7182 (tp30) cc_final: 0.6644 (tp30)
REVERT: Q  323 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7968 (mtt-85)
REVERT: Q  407 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7934 (tppt)
  outliers start: 37
  outliers final: 16
  residues processed: 206
  average time/residue: 0.5537
  time to fit residues: 121.5927
Evaluate side-chains
  209 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue   16 TRP
Chi-restraints excluded: chain K residue   20 LEU
Chi-restraints excluded: chain K residue  100 GLN
Chi-restraints excluded: chain K residue  189 LYS
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  290 SER
Chi-restraints excluded: chain K residue  327 VAL
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  334 LEU
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  390 LEU
Chi-restraints excluded: chain K residue  391 LYS
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  199 GLU
Chi-restraints excluded: chain Q residue   10 ILE
Chi-restraints excluded: chain Q residue  100 ILE
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  323 ARG
Chi-restraints excluded: chain Q residue  357 SER
Chi-restraints excluded: chain Q residue  377 LEU
Chi-restraints excluded: chain Q residue  407 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   chunk 42 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 9 optimal weight:    0.3980
   overall best weight:    4.4788

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

Flipped N/Q/H residues before XYZ refinement:
** K  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.113756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.093918 restraints weight = 18647.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 1.41
r_work: 0.2804 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.1020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9199  Z= 0.208
  Angle     :  0.633   8.010  12528  Z= 0.337
  Chirality :  0.044   0.158   1491
  Planarity :  0.005   0.043   1505
  Dihedral  :  9.037 122.834   1588
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 11.59 %
    Favored  : 84.44 %
  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 aren not related in a simple way.
  whole:  2.00 (0.23), residues: 1143
  helix:  1.97 (0.17), residues: 806
  sheet:  None (None), residues: 0
  loop : -0.18 (0.31), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 154 
 TYR   0.021   0.003   TYR Q 244 
 PHE   0.022   0.002   PHE L  54 
 TRP   0.010   0.002   TRP K  16 
 HIS   0.005   0.001   HIS Q 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 9199)
  covalent geometry    : angle       0.63341 (12528)
  hydrogen bonds       : bond        0.06676 (  658)
  hydrogen bonds       : angle       5.17207 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 189
  time to evaluate  : 0.344 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7087 (mtt90)
REVERT: K  100 GLN cc_start: 0.5588 (OUTLIER) cc_final: 0.5036 (tp-100)
REVERT: K  329 HIS cc_start: 0.6339 (OUTLIER) cc_final: 0.5836 (m-70)
REVERT: K  364 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6706 (mm)
REVERT: K  382 LEU cc_start: 0.8308 (mt) cc_final: 0.7752 (tp)
REVERT: K  390 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7586 (mp)
REVERT: L  199 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7110 (pm20)
REVERT: L  202 GLU cc_start: 0.8292 (tt0) cc_final: 0.8057 (tt0)
REVERT: L  305 MET cc_start: 0.8408 (ttm) cc_final: 0.8173 (ttp)
REVERT: Q  196 LYS cc_start: 0.7821 (mmmm) cc_final: 0.7376 (mmpt)
REVERT: Q  199 GLU cc_start: 0.7717 (pt0) cc_final: 0.7369 (pp20)
REVERT: Q  231 GLU cc_start: 0.7215 (tp30) cc_final: 0.6680 (tp30)
REVERT: Q  323 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8003 (mtt-85)
  outliers start: 37
  outliers final: 20
  residues processed: 205
  average time/residue: 0.5695
  time to fit residues: 124.3307
Evaluate side-chains
  216 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 189
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue   16 TRP
Chi-restraints excluded: chain K residue   20 LEU
Chi-restraints excluded: chain K residue  100 GLN
Chi-restraints excluded: chain K residue  189 LYS
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  290 SER
Chi-restraints excluded: chain K residue  327 VAL
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  334 LEU
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  386 LEU
Chi-restraints excluded: chain K residue  390 LEU
Chi-restraints excluded: chain K residue  391 LYS
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain L residue  199 GLU
Chi-restraints excluded: chain Q residue   10 ILE
Chi-restraints excluded: chain Q residue  100 ILE
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  283 VAL
Chi-restraints excluded: chain Q residue  323 ARG
Chi-restraints excluded: chain Q residue  357 SER
Chi-restraints excluded: chain Q residue  377 LEU
Chi-restraints excluded: chain Q residue  407 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 87 optimal weight:    4.9990
   chunk 46 optimal weight:   10.0000
   chunk 112 optimal weight:    8.9990
   chunk 74 optimal weight:    0.0570
   chunk 18 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 44 optimal weight:    7.9990
   chunk 109 optimal weight:    0.9990
   chunk 60 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    3.2106

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

Flipped N/Q/H residues before XYZ refinement:
** K  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.115274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.097027 restraints weight = 14090.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.16
r_work: 0.2843 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9199  Z= 0.173
  Angle     :  0.589   7.582  12528  Z= 0.314
  Chirality :  0.042   0.138   1491
  Planarity :  0.005   0.041   1505
  Dihedral  :  8.273  92.295   1588
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 12.23 %
    Favored  : 84.12 %
  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 aren not related in a simple way.
  whole:  2.17 (0.24), residues: 1143
  helix:  2.09 (0.17), residues: 808
  sheet:  None (None), residues: 0
  loop : -0.14 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 154 
 TYR   0.021   0.002   TYR Q 244 
 PHE   0.018   0.002   PHE L  54 
 TRP   0.010   0.002   TRP K  16 
 HIS   0.004   0.001   HIS Q 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 9199)
  covalent geometry    : angle       0.58902 (12528)
  hydrogen bonds       : bond        0.06167 (  658)
  hydrogen bonds       : angle       5.07552 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 194
  time to evaluate  : 0.340 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7035 (mtt90)
REVERT: K   16 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.5613 (t-100)
REVERT: K  100 GLN cc_start: 0.5576 (OUTLIER) cc_final: 0.5104 (tp-100)
REVERT: K  201 ARG cc_start: 0.8271 (mmt180) cc_final: 0.7894 (tpp-160)
REVERT: K  329 HIS cc_start: 0.6310 (OUTLIER) cc_final: 0.5746 (m-70)
REVERT: K  364 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6724 (mm)
REVERT: K  382 LEU cc_start: 0.8295 (mt) cc_final: 0.7880 (tp)
REVERT: K  390 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7585 (mp)
REVERT: L   48 PHE cc_start: 0.6922 (t80) cc_final: 0.6669 (t80)
REVERT: L  199 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7046 (pm20)
REVERT: L  202 GLU cc_start: 0.8237 (tt0) cc_final: 0.8005 (tt0)
REVERT: L  305 MET cc_start: 0.8363 (ttm) cc_final: 0.8132 (ttp)
REVERT: Q  196 LYS cc_start: 0.7852 (mmmm) cc_final: 0.7380 (mmpt)
REVERT: Q  199 GLU cc_start: 0.7643 (pt0) cc_final: 0.7309 (pp20)
REVERT: Q  231 GLU cc_start: 0.7164 (tp30) cc_final: 0.6623 (tp30)
REVERT: Q  323 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7957 (mtt-85)
  outliers start: 34
  outliers final: 14
  residues processed: 209
  average time/residue: 0.5499
  time to fit residues: 122.3713
Evaluate side-chains
  214 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 192
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue   16 TRP
Chi-restraints excluded: chain K residue   20 LEU
Chi-restraints excluded: chain K residue  100 GLN
Chi-restraints excluded: chain K residue  189 LYS
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  290 SER
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  334 LEU
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  386 LEU
Chi-restraints excluded: chain K residue  390 LEU
Chi-restraints excluded: chain K residue  391 LYS
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain L residue  199 GLU
Chi-restraints excluded: chain Q residue   10 ILE
Chi-restraints excluded: chain Q residue  100 ILE
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  323 ARG
Chi-restraints excluded: chain Q residue  357 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 104 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 83 optimal weight:    0.7980
   chunk 109 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 114 optimal weight:    6.9990
   chunk 110 optimal weight:    4.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** K  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.116041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.096745 restraints weight = 15967.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.36
r_work: 0.2846 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2744 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9199  Z= 0.162
  Angle     :  0.573   7.291  12528  Z= 0.305
  Chirality :  0.041   0.139   1491
  Planarity :  0.004   0.041   1505
  Dihedral  :  7.407  59.609   1585
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 13.20 %
    Favored  : 83.37 %
  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 aren not related in a simple way.
  whole:  2.25 (0.24), residues: 1143
  helix:  2.16 (0.17), residues: 808
  sheet:  None (None), residues: 0
  loop : -0.14 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K 154 
 TYR   0.020   0.002   TYR Q 244 
 PHE   0.017   0.002   PHE L  54 
 TRP   0.010   0.002   TRP K  16 
 HIS   0.004   0.001   HIS Q 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9199)
  covalent geometry    : angle       0.57273 (12528)
  hydrogen bonds       : bond        0.05951 (  658)
  hydrogen bonds       : angle       5.03087 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 193
  time to evaluate  : 0.219 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7007 (mtt90)
REVERT: K   16 TRP cc_start: 0.7570 (OUTLIER) cc_final: 0.5610 (t-100)
REVERT: K  100 GLN cc_start: 0.5571 (OUTLIER) cc_final: 0.5219 (tp-100)
REVERT: K  201 ARG cc_start: 0.8286 (mmt180) cc_final: 0.7906 (tpp-160)
REVERT: K  329 HIS cc_start: 0.6309 (OUTLIER) cc_final: 0.5732 (m-70)
REVERT: K  364 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6739 (mm)
REVERT: K  379 THR cc_start: 0.8325 (m) cc_final: 0.8052 (t)
REVERT: K  382 LEU cc_start: 0.8294 (mt) cc_final: 0.7879 (tp)
REVERT: K  390 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7563 (mp)
REVERT: L   48 PHE cc_start: 0.6874 (t80) cc_final: 0.6531 (t80)
REVERT: L  199 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7157 (pm20)
REVERT: L  202 GLU cc_start: 0.8248 (tt0) cc_final: 0.8019 (tt0)
REVERT: L  305 MET cc_start: 0.8352 (ttm) cc_final: 0.8116 (ttp)
REVERT: Q  196 LYS cc_start: 0.7853 (mmmm) cc_final: 0.7357 (mmpt)
REVERT: Q  199 GLU cc_start: 0.7659 (pt0) cc_final: 0.7323 (pp20)
REVERT: Q  231 GLU cc_start: 0.7159 (tp30) cc_final: 0.6621 (tp30)
REVERT: Q  323 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7968 (mtt-85)
  outliers start: 32
  outliers final: 15
  residues processed: 207
  average time/residue: 0.5580
  time to fit residues: 122.8473
Evaluate side-chains
  215 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 192
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue   16 TRP
Chi-restraints excluded: chain K residue   20 LEU
Chi-restraints excluded: chain K residue  100 GLN
Chi-restraints excluded: chain K residue  189 LYS
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  290 SER
Chi-restraints excluded: chain K residue  327 VAL
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  386 LEU
Chi-restraints excluded: chain K residue  390 LEU
Chi-restraints excluded: chain K residue  391 LYS
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain L residue  199 GLU
Chi-restraints excluded: chain Q residue   10 ILE
Chi-restraints excluded: chain Q residue  100 ILE
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  323 ARG
Chi-restraints excluded: chain Q residue  357 SER
Chi-restraints excluded: chain Q residue  377 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 106 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** K  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.115676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.095868 restraints weight = 18984.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.46
r_work: 0.2831 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2718
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9199  Z= 0.169
  Angle     :  0.581   8.012  12528  Z= 0.310
  Chirality :  0.041   0.134   1491
  Planarity :  0.004   0.040   1505
  Dihedral  :  7.344  60.067   1585
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 13.52 %
    Favored  : 82.94 %
  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 aren not related in a simple way.
  whole:  2.24 (0.24), residues: 1143
  helix:  2.16 (0.17), residues: 808
  sheet:  None (None), residues: 0
  loop : -0.14 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 154 
 TYR   0.020   0.002   TYR Q 244 
 PHE   0.018   0.002   PHE L  54 
 TRP   0.010   0.002   TRP K  16 
 HIS   0.004   0.001   HIS Q 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9199)
  covalent geometry    : angle       0.58118 (12528)
  hydrogen bonds       : bond        0.06061 (  658)
  hydrogen bonds       : angle       5.04798 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 187
  time to evaluate  : 0.325 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7018 (mtt90)
REVERT: K   16 TRP cc_start: 0.7585 (OUTLIER) cc_final: 0.5566 (t-100)
REVERT: K  100 GLN cc_start: 0.5557 (OUTLIER) cc_final: 0.5315 (tp-100)
REVERT: K  201 ARG cc_start: 0.8343 (mmt180) cc_final: 0.7917 (tpp-160)
REVERT: K  329 HIS cc_start: 0.6291 (OUTLIER) cc_final: 0.5738 (m-70)
REVERT: K  364 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6741 (mm)
REVERT: K  379 THR cc_start: 0.8332 (m) cc_final: 0.8049 (t)
REVERT: K  382 LEU cc_start: 0.8306 (mt) cc_final: 0.7893 (tp)
REVERT: K  390 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7614 (mp)
REVERT: L   48 PHE cc_start: 0.6882 (t80) cc_final: 0.6556 (t80)
REVERT: L  199 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7181 (pm20)
REVERT: L  202 GLU cc_start: 0.8280 (tt0) cc_final: 0.8052 (tt0)
REVERT: L  305 MET cc_start: 0.8359 (ttm) cc_final: 0.8119 (ttp)
REVERT: Q  196 LYS cc_start: 0.7850 (mmmm) cc_final: 0.7349 (mmpt)
REVERT: Q  199 GLU cc_start: 0.7703 (pt0) cc_final: 0.7372 (pp20)
REVERT: Q  231 GLU cc_start: 0.7177 (tp30) cc_final: 0.6633 (tp30)
REVERT: Q  323 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7985 (mtt-85)
  outliers start: 33
  outliers final: 16
  residues processed: 202
  average time/residue: 0.5593
  time to fit residues: 120.5046
Evaluate side-chains
  210 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 186
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue   16 TRP
Chi-restraints excluded: chain K residue  100 GLN
Chi-restraints excluded: chain K residue  189 LYS
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  290 SER
Chi-restraints excluded: chain K residue  327 VAL
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  386 LEU
Chi-restraints excluded: chain K residue  390 LEU
Chi-restraints excluded: chain K residue  391 LYS
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain L residue  199 GLU
Chi-restraints excluded: chain Q residue   10 ILE
Chi-restraints excluded: chain Q residue  100 ILE
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  283 VAL
Chi-restraints excluded: chain Q residue  323 ARG
Chi-restraints excluded: chain Q residue  357 SER
Chi-restraints excluded: chain Q residue  377 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 30 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 105 optimal weight:    3.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** K  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.113644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.094339 restraints weight = 16042.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 1.35
r_work: 0.2815 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   9199  Z= 0.218
  Angle     :  0.646   9.080  12528  Z= 0.342
  Chirality :  0.045   0.151   1491
  Planarity :  0.005   0.041   1505
  Dihedral  :  7.784  64.376   1585
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 13.41 %
    Favored  : 83.15 %
  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 aren not related in a simple way.
  whole:  2.03 (0.24), residues: 1143
  helix:  2.00 (0.17), residues: 806
  sheet:  None (None), residues: 0
  loop : -0.20 (0.31), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 154 
 TYR   0.021   0.003   TYR L 180 
 PHE   0.022   0.003   PHE L  54 
 TRP   0.015   0.002   TRP K 220 
 HIS   0.006   0.002   HIS Q 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 9199)
  covalent geometry    : angle       0.64552 (12528)
  hydrogen bonds       : bond        0.06738 (  658)
  hydrogen bonds       : angle       5.17311 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 189
  time to evaluate  : 0.383 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7064 (mtt90)
REVERT: K  201 ARG cc_start: 0.8368 (mmt180) cc_final: 0.7935 (tpp-160)
REVERT: K  329 HIS cc_start: 0.6308 (OUTLIER) cc_final: 0.5853 (m-70)
REVERT: K  364 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6692 (mm)
REVERT: K  382 LEU cc_start: 0.8308 (mt) cc_final: 0.7904 (tp)
REVERT: K  390 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7627 (mp)
REVERT: L   48 PHE cc_start: 0.6981 (t80) cc_final: 0.6757 (t80)
REVERT: L  199 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7156 (pm20)
REVERT: L  202 GLU cc_start: 0.8246 (tt0) cc_final: 0.8008 (tt0)
REVERT: L  305 MET cc_start: 0.8379 (ttm) cc_final: 0.8144 (ttp)
REVERT: Q  196 LYS cc_start: 0.7831 (mmmm) cc_final: 0.7376 (mmpt)
REVERT: Q  199 GLU cc_start: 0.7669 (pt0) cc_final: 0.7326 (pp20)
REVERT: Q  231 GLU cc_start: 0.7190 (tp30) cc_final: 0.6646 (tp30)
REVERT: Q  323 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7984 (mtt-85)
  outliers start: 32
  outliers final: 16
  residues processed: 206
  average time/residue: 0.6626
  time to fit residues: 146.0042
Evaluate side-chains
  213 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 191
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue   16 TRP
Chi-restraints excluded: chain K residue  189 LYS
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  290 SER
Chi-restraints excluded: chain K residue  327 VAL
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  386 LEU
Chi-restraints excluded: chain K residue  390 LEU
Chi-restraints excluded: chain K residue  391 LYS
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain L residue  199 GLU
Chi-restraints excluded: chain Q residue   10 ILE
Chi-restraints excluded: chain Q residue  100 ILE
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  283 VAL
Chi-restraints excluded: chain Q residue  323 ARG
Chi-restraints excluded: chain Q residue  357 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 111 optimal weight:    4.9990
   chunk 114 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 85 optimal weight:    8.9990
   chunk 93 optimal weight:    9.9990
   chunk 33 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** K  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 100 GLN
L  58 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.118283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.098720 restraints weight = 14216.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 1.25
r_work: 0.2886 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2780 r_free = 0.2780    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9199  Z= 0.139
  Angle     :  0.542   8.397  12528  Z= 0.288
  Chirality :  0.039   0.129   1491
  Planarity :  0.004   0.041   1505
  Dihedral  :  6.837  55.102   1582
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.70 %
    Favored  : 82.94 %
  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 aren not related in a simple way.
  whole:  2.43 (0.24), residues: 1143
  helix:  2.29 (0.17), residues: 815
  sheet:  None (None), residues: 0
  loop : -0.11 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 154 
 TYR   0.019   0.002   TYR Q 244 
 PHE   0.016   0.002   PHE L 294 
 TRP   0.011   0.001   TRP K 220 
 HIS   0.005   0.001   HIS L  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9199)
  covalent geometry    : angle       0.54170 (12528)
  hydrogen bonds       : bond        0.05392 (  658)
  hydrogen bonds       : angle       4.95198 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 196
  time to evaluate  : 0.377 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6972 (mtt90)
REVERT: K  201 ARG cc_start: 0.8311 (mmt180) cc_final: 0.7955 (tpp-160)
REVERT: K  329 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5674 (m-70)
REVERT: K  364 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6764 (mm)
REVERT: K  379 THR cc_start: 0.8304 (m) cc_final: 0.8038 (t)
REVERT: K  382 LEU cc_start: 0.8282 (mt) cc_final: 0.7758 (tp)
REVERT: K  390 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7602 (mp)
REVERT: L   48 PHE cc_start: 0.6811 (t80) cc_final: 0.6125 (t80)
REVERT: L  202 GLU cc_start: 0.8252 (tt0) cc_final: 0.8038 (tt0)
REVERT: L  305 MET cc_start: 0.8243 (ttm) cc_final: 0.8013 (ttp)
REVERT: Q  101 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7440 (mp)
REVERT: Q  196 LYS cc_start: 0.7846 (mmmm) cc_final: 0.7474 (mtmt)
REVERT: Q  199 GLU cc_start: 0.7675 (pt0) cc_final: 0.7340 (pp20)
REVERT: Q  231 GLU cc_start: 0.7147 (tp30) cc_final: 0.6700 (tp30)
REVERT: Q  323 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7954 (mtt-85)
REVERT: Q  407 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7912 (tppt)
  outliers start: 22
  outliers final: 13
  residues processed: 207
  average time/residue: 0.6461
  time to fit residues: 142.9789
Evaluate side-chains
  210 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 191
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue  189 LYS
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  290 SER
Chi-restraints excluded: chain K residue  327 VAL
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  390 LEU
Chi-restraints excluded: chain K residue  391 LYS
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain Q residue   10 ILE
Chi-restraints excluded: chain Q residue  100 ILE
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  323 ARG
Chi-restraints excluded: chain Q residue  357 SER
Chi-restraints excluded: chain Q residue  377 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0770
   chunk 107 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0470
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    1.0242

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

Flipped N/Q/H residues before XYZ refinement:
K  49 GLN
L  58 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.120995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.104177 restraints weight = 10257.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 0.95
r_work: 0.2963 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 2.32 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9199  Z= 0.125
  Angle     :  0.524   9.366  12528  Z= 0.276
  Chirality :  0.038   0.124   1491
  Planarity :  0.004   0.040   1505
  Dihedral  :  6.281  54.742   1577
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.91 %
    Favored  : 82.73 %
  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 aren not related in a simple way.
  whole:  2.60 (0.24), residues: 1143
  helix:  2.44 (0.17), residues: 816
  sheet:  None (None), residues: 0
  loop : -0.11 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 154 
 TYR   0.018   0.002   TYR Q 244 
 PHE   0.017   0.001   PHE L 294 
 TRP   0.013   0.001   TRP K 220 
 HIS   0.005   0.001   HIS L  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9199)
  covalent geometry    : angle       0.52403 (12528)
  hydrogen bonds       : bond        0.04952 (  658)
  hydrogen bonds       : angle       4.86183 ( 1933)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 196
  time to evaluate  : 0.399 
Fit side-chains
REVERT: K   11 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6909 (mtt90)
REVERT: K  201 ARG cc_start: 0.8247 (mmt180) cc_final: 0.7906 (tpp-160)
REVERT: K  304 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8231 (mt)
REVERT: K  329 HIS cc_start: 0.6225 (OUTLIER) cc_final: 0.5607 (m-70)
REVERT: K  364 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6812 (mm)
REVERT: K  379 THR cc_start: 0.8303 (m) cc_final: 0.8026 (t)
REVERT: K  382 LEU cc_start: 0.8254 (mt) cc_final: 0.7729 (tp)
REVERT: L   48 PHE cc_start: 0.6745 (t80) cc_final: 0.6097 (t80)
REVERT: L  202 GLU cc_start: 0.8144 (tt0) cc_final: 0.7925 (tt0)
REVERT: L  305 MET cc_start: 0.8120 (ttm) cc_final: 0.7896 (ttp)
REVERT: Q  101 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7455 (mp)
REVERT: Q  196 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7548 (mtmt)
REVERT: Q  199 GLU cc_start: 0.7564 (pt0) cc_final: 0.7268 (pp20)
REVERT: Q  231 GLU cc_start: 0.7017 (tp30) cc_final: 0.6622 (tp30)
REVERT: Q  323 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7864 (mtt-85)
REVERT: Q  407 LYS cc_start: 0.8243 (ttmt) cc_final: 0.7866 (tppt)
  outliers start: 22
  outliers final: 12
  residues processed: 205
  average time/residue: 0.6666
  time to fit residues: 145.9752
Evaluate side-chains
  212 residues out of total 933 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 194
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   11 ARG
Chi-restraints excluded: chain K residue  223 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  290 SER
Chi-restraints excluded: chain K residue  304 ILE
Chi-restraints excluded: chain K residue  327 VAL
Chi-restraints excluded: chain K residue  329 HIS
Chi-restraints excluded: chain K residue  364 LEU
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  391 LYS
Chi-restraints excluded: chain L residue  100 ILE
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain Q residue   10 ILE
Chi-restraints excluded: chain Q residue  100 ILE
Chi-restraints excluded: chain Q residue  101 LEU
Chi-restraints excluded: chain Q residue  323 ARG
Chi-restraints excluded: chain Q residue  357 SER
Chi-restraints excluded: chain Q residue  377 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 98 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 87 optimal weight:    5.9990
   chunk 63 optimal weight:    9.9990
   chunk 105 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** K  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  58 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.113953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.095028 restraints weight = 14152.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 1.26
r_work: 0.2822 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9199  Z= 0.226
  Angle     :  0.664   9.508  12528  Z= 0.350
  Chirality :  0.045   0.147   1491
  Planarity :  0.005   0.041   1505
  Dihedral  :  7.090  59.525   1573
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.24 %
    Favored  : 82.51 %
  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 aren not related in a simple way.
  whole:  2.11 (0.24), residues: 1143
  helix:  2.05 (0.17), residues: 808
  sheet:  None (None), residues: 0
  loop : -0.17 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K 154 
 TYR   0.021   0.003   TYR L 180 
 PHE   0.024   0.003   PHE L  54 
 TRP   0.031   0.003   TRP K 220 
 HIS   0.006   0.002   HIS Q 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 9199)
  covalent geometry    : angle       0.66376 (12528)
  hydrogen bonds       : bond        0.06820 (  658)
  hydrogen bonds       : angle       5.17201 ( 1933)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4360.20 seconds
wall clock time: 74 minutes 59.89 seconds (4499.89 seconds total)