Starting phenix.real_space_refine
on Tue Mar  3 19:41:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uxa_26856/03_2026/7uxa_26856.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uxa_26856/03_2026/7uxa_26856.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uxa_26856/03_2026/7uxa_26856.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uxa_26856/03_2026/7uxa_26856.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uxa_26856/03_2026/7uxa_26856.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uxa_26856/03_2026/7uxa_26856.map"
  }
  resolution = 3.28
  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=   0.001 sd=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      77      5.49       5
     Mg      2      5.21       5
     S      26      5.16       5
     C    4890      2.51       5
     N    1420      2.21       5
     O    1705      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8120
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1762
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 212}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 971
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 8, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1615
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 8, 'TRANS': 191}
          Chain breaks: 1
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 2105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2105
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 16, 'TRANS': 247}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "E"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 1665
          Inner-chain residues flagged as termini: ['pdbres="  A E  47 "']
          Classifications: {'RNA': 78}
          Modifications used: {'5*END': 1, 'p5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 13, 'rna3p': 64}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.97, per 1000 atoms: 0.24
  Number of scatterers: 8120
  At special positions: 0
  Unit cell: (87.608, 86.676, 123.024, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      26     16.00
     P      77     15.00
     Mg      2     11.99
     O    1705      8.00
     N    1420      7.00
     C    4890      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: 0.71
  Conformation dependent library (CDL) restraints added in 253.6 milliseconds
  

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1530

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      35.4% alpha, 16.3% beta
      27 base pairs and 38 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 25
    Processing helix  chain 'A' and resid 53 through 63
    Processing helix  chain 'A' and resid 83 through 101
      removed outlier: 3.593A  pdb=" N   GLN A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLU A  96 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 230
      removed outlier: 3.608A  pdb=" N   ASP A 226 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
    Processing helix  chain 'A' and resid 270 through 285
    Processing helix  chain 'B' and resid 44 through 53
      removed outlier: 4.314A  pdb=" N   GLU B  48 " --> pdb=" O   PRO B  44 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ASP B  53 " --> pdb=" O   MET B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 73
    Processing helix  chain 'B' and resid 116 through 131
    Processing helix  chain 'C' and resid 53 through 63
    Processing helix  chain 'C' and resid 300 through 310
    Processing helix  chain 'C' and resid 324 through 336
    Processing helix  chain 'C' and resid 338 through 349
    Processing helix  chain 'C' and resid 400 through 414
    Processing helix  chain 'C' and resid 430 through 443
      removed outlier: 3.824A  pdb=" N   GLU C 435 " --> pdb=" O   LYS C 432 " (cutoff:3.500A)
      Proline residue:  C 437  - end of helix
      removed outlier: 3.622A  pdb=" N   ILE C 443 " --> pdb=" O   MET C 440 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 27
      removed outlier: 3.851A  pdb=" N   ARG D  27 " --> pdb=" O   LEU D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 67
      removed outlier: 3.707A  pdb=" N   ALA D  52 " --> pdb=" O   SER D  48 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLU D  53 " --> pdb=" O   ALA D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 77
      No H-bonds generated for 'chain 'D' and resid 75 through 77'
    Processing helix  chain 'D' and resid 96 through 101
      removed outlier: 3.611A  pdb=" N   THR D 101 " --> pdb=" O   PHE D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 124
    Processing helix  chain 'D' and resid 136 through 145
      removed outlier: 3.673A  pdb=" N   LEU D 145 " --> pdb=" O   TYR D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 163
    Processing helix  chain 'D' and resid 454 through 459
      removed outlier: 3.842A  pdb=" N   ALA D 459 " --> pdb=" O   ASP D 456 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 484 through 495
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32
      removed outlier: 4.512A  pdb=" N   SER A  11 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LEU A   2 " --> pdb=" O   THR A  67 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   VAL A  69 " --> pdb=" O   LEU A   2 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   VAL A   4 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 187
      removed outlier: 3.524A  pdb=" N   GLU D  72 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ARG D  70 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 235
      removed outlier: 4.610A  pdb=" N   LEU A 289 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   CYS A 291 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 235
      removed outlier: 4.610A  pdb=" N   LEU A 289 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   CYS A 291 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU A 288 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   THR B 104 " --> pdb=" O   THR B 140 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   ALA B 142 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   VAL B 106 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   VAL B 144 " --> pdb=" O   VAL B 106 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   THR B 108 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   ILE B  90 " --> pdb=" O   PRO B 107 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 268 through 269
      removed outlier: 4.115A  pdb=" N   LEU B 114 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 297 through 299
      removed outlier: 3.850A  pdb=" N   VAL C  49 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   PHE C  40 " --> pdb=" O   SER C 315 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TYR C 317 " --> pdb=" O   PHE C  40 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ALA C  42 " --> pdb=" O   TYR C 317 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358
      removed outlier: 4.025A  pdb=" N   TYR C 380 " --> pdb=" O   LEU C 368 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 385 through 387
      removed outlier: 3.540A  pdb=" N   LEU C 423 " --> pdb=" O   GLU C 385 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   GLU C 447 " --> pdb=" O   PHE D 518 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   CYS D 474 " --> pdb=" O   ALA D 503 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   VAL D 505 " --> pdb=" O   CYS D 474 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   SER D 476 " --> pdb=" O   VAL D 505 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 104 through 106

    264 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      68 hydrogen bonds
      110 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      38 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2137
        1.33 -     1.45: 1945
        1.45 -     1.57: 4193
        1.57 -     1.69: 153
        1.69 -     1.81: 41
  Bond restraints: 8469
  Sorted by residual:
  bond pdb=" CA  GLY B  94 "
       pdb=" C   GLY B  94 "
    ideal  model  delta    sigma   weight residual
    1.521  1.511  0.011 1.13e-02 7.83e+03 8.78e-01
  bond pdb=" CB  TRP D  99 "
       pdb=" CG  TRP D  99 "
    ideal  model  delta    sigma   weight residual
    1.498  1.470  0.028 3.10e-02 1.04e+03 8.02e-01
  bond pdb=" CA  ALA A 286 "
       pdb=" C   ALA A 286 "
    ideal  model  delta    sigma   weight residual
    1.522  1.531 -0.009 1.08e-02 8.57e+03 6.87e-01
  bond pdb=" CA  ALA C 377 "
       pdb=" C   ALA C 377 "
    ideal  model  delta    sigma   weight residual
    1.531  1.522  0.009 1.12e-02 7.97e+03 6.49e-01
  bond pdb=" CA  GLU C 458 "
       pdb=" C   GLU C 458 "
    ideal  model  delta    sigma   weight residual
    1.530  1.521  0.009 1.10e-02 8.26e+03 6.09e-01
  ... (remaining 8464 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 11286
        1.19 -     2.38: 463
        2.38 -     3.57: 105
        3.57 -     4.76: 13
        4.76 -     5.95: 2
  Bond angle restraints: 11869
  Sorted by residual:
  angle pdb=" N   ASP A 243 "
        pdb=" CA  ASP A 243 "
        pdb=" C   ASP A 243 "
      ideal   model   delta    sigma   weight residual
     114.75  111.06    3.69 1.26e+00 6.30e-01 8.60e+00
  angle pdb=" N   THR D 429 "
        pdb=" CA  THR D 429 "
        pdb=" C   THR D 429 "
      ideal   model   delta    sigma   weight residual
     107.23  111.62   -4.39 1.67e+00 3.59e-01 6.92e+00
  angle pdb=" N   LYS C 371 "
        pdb=" CA  LYS C 371 "
        pdb=" C   LYS C 371 "
      ideal   model   delta    sigma   weight residual
     108.19  111.38   -3.19 1.29e+00 6.01e-01 6.13e+00
  angle pdb=" N   TYR C 362 "
        pdb=" CA  TYR C 362 "
        pdb=" C   TYR C 362 "
      ideal   model   delta    sigma   weight residual
     109.65  105.95    3.70 1.56e+00 4.11e-01 5.64e+00
  angle pdb=" N   VAL C 335 "
        pdb=" CA  VAL C 335 "
        pdb=" C   VAL C 335 "
      ideal   model   delta    sigma   weight residual
     113.07  110.04    3.03 1.36e+00 5.41e-01 4.97e+00
  ... (remaining 11864 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.49: 4821
       24.49 -    48.98: 204
       48.98 -    73.47: 139
       73.47 -    97.97: 11
       97.97 -   122.46: 3
  Dihedral angle restraints: 5178
    sinusoidal: 2805
      harmonic: 2373
  Sorted by residual:
  dihedral pdb=" CA  LEU C 360 "
           pdb=" C   LEU C 360 "
           pdb=" N   LYS C 361 "
           pdb=" CA  LYS C 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.82   20.18     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" O4'   G E  72 "
           pdb=" C1'   G E  72 "
           pdb=" N9    G E  72 "
           pdb=" C4    G E  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -19.43  -70.57     1      2.00e+01 2.50e-03 1.60e+01
  dihedral pdb=" O4'   A E  52 "
           pdb=" C1'   A E  52 "
           pdb=" N9    A E  52 "
           pdb=" C4    A E  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -158.89   52.89     1      1.70e+01 3.46e-03 1.32e+01
  ... (remaining 5175 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1053
       0.037 -    0.074: 249
       0.074 -    0.111: 69
       0.111 -    0.147: 12
       0.147 -    0.184: 1
  Chirality restraints: 1384
  Sorted by residual:
  chirality pdb=" C1'   A E  74 "
            pdb=" O4'   A E  74 "
            pdb=" C2'   A E  74 "
            pdb=" N9    A E  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.27    0.18 2.00e-01 2.50e+01 8.48e-01
  chirality pdb=" C1'   G E  22 "
            pdb=" O4'   G E  22 "
            pdb=" C2'   G E  22 "
            pdb=" N9    G E  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE B  90 "
            pdb=" N   ILE B  90 "
            pdb=" C   ILE B  90 "
            pdb=" CB  ILE B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  ... (remaining 1381 not shown)

  Planarity restraints: 1229
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 373 "   -0.036 5.00e-02 4.00e+02   5.36e-02 4.60e+00
        pdb=" N   PRO C 374 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 374 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 374 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A E  74 "    0.024 2.00e-02 2.50e+03   1.10e-02 3.32e+00
        pdb=" N9    A E  74 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8    A E  74 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A E  74 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A E  74 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A E  74 "    0.001 2.00e-02 2.50e+03
        pdb=" N6    A E  74 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    A E  74 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A E  74 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A E  74 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A E  74 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U E   6 "   -0.020 2.00e-02 2.50e+03   1.08e-02 2.61e+00
        pdb=" N1    U E   6 "    0.024 2.00e-02 2.50e+03
        pdb=" C2    U E   6 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    U E   6 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U E   6 "    0.000 2.00e-02 2.50e+03
        pdb=" C4    U E   6 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4    U E   6 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    U E   6 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    U E   6 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1226 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 142
        2.65 -     3.21: 7217
        3.21 -     3.77: 13257
        3.77 -     4.34: 17916
        4.34 -     4.90: 28118
  Nonbonded interactions: 66650
  Sorted by model distance:
  nonbonded pdb=" OP1   G E   9 "
            pdb="MG    MG E 101 "
     model   vdw
     2.084 2.170
  nonbonded pdb=" OG  SER D 495 "
            pdb=" O   VAL D 498 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" OE1 GLU A  62 "
            pdb=" OH  TYR A 221 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" NH2 ARG D  27 "
            pdb=" OP1   G E  17 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" OE1 GLU D 122 "
            pdb=" OH  TYR D 155 "
     model   vdw
     2.255 3.040
  ... (remaining 66645 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.920
  Find NCS groups from input model:        0.040
  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:1.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8469  Z= 0.165
  Angle     :  0.577   5.955  11869  Z= 0.330
  Chirality :  0.036   0.184   1384
  Planarity :  0.004   0.054   1229
  Dihedral  : 16.774 122.458   3648
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.00 %
    Favored  : 93.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.31), residues: 805
  helix:  0.29 (0.31), residues: 276
  sheet: -1.95 (0.45), residues: 128
  loop : -0.75 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 220 
 TYR   0.010   0.001   TYR D 155 
 PHE   0.013   0.001   PHE A 244 
 TRP   0.011   0.001   TRP D  99 
 HIS   0.003   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8469)
  covalent geometry    : angle       0.57696 (11869)
  hydrogen bonds       : bond        0.14263 (  323)
  hydrogen bonds       : angle       5.92833 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 155
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7644 (mmt-90) cc_final: 0.7116 (mtp180)
REVERT: B   59 GLN cc_start: 0.8097 (mt0) cc_final: 0.7868 (mp10)
REVERT: B   81 CYS cc_start: 0.9034 (m) cc_final: 0.8592 (p)
REVERT: B  147 ASP cc_start: 0.8943 (t0) cc_final: 0.8663 (t0)
REVERT: B  161 LEU cc_start: 0.8177 (mt) cc_final: 0.7880 (pt)
REVERT: C   46 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7287 (m-40)
REVERT: C   58 GLU cc_start: 0.5999 (mt-10) cc_final: 0.4965 (tp30)
REVERT: C  317 TYR cc_start: 0.6729 (m-80) cc_final: 0.6519 (m-80)
REVERT: C  367 LEU cc_start: 0.8298 (mt) cc_final: 0.7883 (mp)
REVERT: C  429 MET cc_start: 0.6062 (tmm) cc_final: 0.5803 (tmm)
  outliers start: 6
  outliers final: 1
  residues processed: 161
  average time/residue: 0.0906
  time to fit residues: 19.6525
Evaluate side-chains
  106 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 ASN
Chi-restraints excluded: chain C residue  447 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 GLN
C  46 ASN
C  47 ASN
C 413 ASN
D  35 GLN
** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 464 ASN
D 522 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.166735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.128430 restraints weight = 12660.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.32
r_work: 0.3583 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8469  Z= 0.144
  Angle     :  0.534   5.559  11869  Z= 0.274
  Chirality :  0.038   0.166   1384
  Planarity :  0.004   0.050   1229
  Dihedral  : 18.925 116.431   2121
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.42 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.31), residues: 805
  helix:  0.69 (0.32), residues: 272
  sheet: -1.59 (0.45), residues: 134
  loop : -0.49 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 340 
 TYR   0.016   0.001   TYR B  67 
 PHE   0.012   0.001   PHE C 305 
 TRP   0.011   0.001   TRP D  99 
 HIS   0.003   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8469)
  covalent geometry    : angle       0.53364 (11869)
  hydrogen bonds       : bond        0.03958 (  323)
  hydrogen bonds       : angle       4.39124 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 MET cc_start: 0.7850 (tpp) cc_final: 0.7482 (tpt)
REVERT: C   58 GLU cc_start: 0.5882 (mt-10) cc_final: 0.5043 (tp30)
REVERT: C  348 TYR cc_start: 0.7047 (t80) cc_final: 0.6703 (t80)
REVERT: C  413 ASN cc_start: 0.7944 (m-40) cc_final: 0.7716 (m110)
REVERT: C  429 MET cc_start: 0.6069 (tmm) cc_final: 0.5834 (tmm)
REVERT: D  460 THR cc_start: 0.9118 (p) cc_final: 0.8754 (t)
REVERT: D  465 ASN cc_start: 0.7820 (p0) cc_final: 0.7532 (p0)
REVERT: D  509 ASP cc_start: 0.8133 (t0) cc_final: 0.7840 (t70)
  outliers start: 10
  outliers final: 5
  residues processed: 121
  average time/residue: 0.0877
  time to fit residues: 14.3368
Evaluate side-chains
  108 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   47 ASN
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  519 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 156 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.165890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.127586 restraints weight = 12391.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.31
r_work: 0.3577 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8469  Z= 0.142
  Angle     :  0.537   6.097  11869  Z= 0.274
  Chirality :  0.037   0.172   1384
  Planarity :  0.004   0.050   1229
  Dihedral  : 18.797 116.432   2116
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.03 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.31), residues: 805
  helix:  0.83 (0.31), residues: 272
  sheet: -1.40 (0.45), residues: 134
  loop : -0.39 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 214 
 TYR   0.015   0.001   TYR B  67 
 PHE   0.011   0.001   PHE A 233 
 TRP   0.011   0.001   TRP D  63 
 HIS   0.002   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8469)
  covalent geometry    : angle       0.53684 (11869)
  hydrogen bonds       : bond        0.03675 (  323)
  hydrogen bonds       : angle       4.18911 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 GLN cc_start: 0.8026 (mp10) cc_final: 0.7763 (mp10)
REVERT: C   44 MET cc_start: 0.7817 (tpp) cc_final: 0.7562 (tpt)
REVERT: C  348 TYR cc_start: 0.7121 (t80) cc_final: 0.6621 (t80)
REVERT: C  413 ASN cc_start: 0.7895 (m-40) cc_final: 0.7683 (m110)
REVERT: C  419 MET cc_start: 0.7270 (mtt) cc_final: 0.6839 (mtt)
REVERT: C  429 MET cc_start: 0.5921 (tmm) cc_final: 0.5666 (tmm)
REVERT: D   63 TRP cc_start: 0.8542 (m100) cc_final: 0.8225 (m100)
REVERT: D  460 THR cc_start: 0.9103 (p) cc_final: 0.8739 (t)
REVERT: D  465 ASN cc_start: 0.7939 (p0) cc_final: 0.7650 (p0)
  outliers start: 14
  outliers final: 5
  residues processed: 119
  average time/residue: 0.0813
  time to fit residues: 13.3807
Evaluate side-chains
  103 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0570
   chunk 43 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.9102

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN
C  59 GLN
D 156 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.165846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.127144 restraints weight = 12734.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 2.34
r_work: 0.3573 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8469  Z= 0.144
  Angle     :  0.522   5.699  11869  Z= 0.266
  Chirality :  0.037   0.175   1384
  Planarity :  0.004   0.049   1229
  Dihedral  : 18.739 113.571   2116
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.76 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.31), residues: 805
  helix:  1.01 (0.31), residues: 270
  sheet: -1.33 (0.45), residues: 134
  loop : -0.36 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 340 
 TYR   0.013   0.001   TYR D 470 
 PHE   0.014   0.001   PHE A 233 
 TRP   0.009   0.001   TRP C 354 
 HIS   0.002   0.000   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8469)
  covalent geometry    : angle       0.52217 (11869)
  hydrogen bonds       : bond        0.03580 (  323)
  hydrogen bonds       : angle       4.13044 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  205 GLN cc_start: 0.6634 (tm-30) cc_final: 0.6164 (tm-30)
REVERT: B   59 GLN cc_start: 0.8101 (mp10) cc_final: 0.7676 (mp10)
REVERT: B   64 PHE cc_start: 0.8572 (t80) cc_final: 0.8353 (t80)
REVERT: C   44 MET cc_start: 0.7716 (tpp) cc_final: 0.7401 (tpt)
REVERT: C  348 TYR cc_start: 0.7379 (t80) cc_final: 0.6781 (t80)
REVERT: C  413 ASN cc_start: 0.7900 (m-40) cc_final: 0.7657 (m110)
REVERT: C  419 MET cc_start: 0.7255 (mtt) cc_final: 0.6930 (ttm)
REVERT: D   63 TRP cc_start: 0.8497 (m100) cc_final: 0.8218 (m100)
REVERT: D  460 THR cc_start: 0.9082 (p) cc_final: 0.8747 (t)
REVERT: D  465 ASN cc_start: 0.8018 (p0) cc_final: 0.7694 (p0)
  outliers start: 13
  outliers final: 6
  residues processed: 108
  average time/residue: 0.0828
  time to fit residues: 12.5684
Evaluate side-chains
  101 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  325 ILE
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  519 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 85 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  78 HIS
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.157886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.121854 restraints weight = 12689.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.36
r_work: 0.3454 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8469  Z= 0.140
  Angle     :  0.518   5.775  11869  Z= 0.264
  Chirality :  0.037   0.177   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 18.704 111.484   2116
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.64 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.31), residues: 805
  helix:  1.10 (0.31), residues: 270
  sheet: -1.10 (0.46), residues: 132
  loop : -0.33 (0.34), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 214 
 TYR   0.014   0.001   TYR D 470 
 PHE   0.011   0.001   PHE C 305 
 TRP   0.008   0.001   TRP D  99 
 HIS   0.002   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8469)
  covalent geometry    : angle       0.51757 (11869)
  hydrogen bonds       : bond        0.03479 (  323)
  hydrogen bonds       : angle       4.02138 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 PHE cc_start: 0.7725 (t80) cc_final: 0.7476 (t80)
REVERT: A  205 GLN cc_start: 0.6595 (tm-30) cc_final: 0.6102 (tm-30)
REVERT: B   59 GLN cc_start: 0.8110 (mp10) cc_final: 0.7579 (mp10)
REVERT: B  147 ASP cc_start: 0.8796 (t0) cc_final: 0.8538 (t0)
REVERT: C   44 MET cc_start: 0.7816 (tpp) cc_final: 0.7461 (tpt)
REVERT: C  305 PHE cc_start: 0.8026 (t80) cc_final: 0.7820 (t80)
REVERT: C  348 TYR cc_start: 0.7575 (t80) cc_final: 0.6929 (t80)
REVERT: C  413 ASN cc_start: 0.7875 (m-40) cc_final: 0.7611 (m110)
REVERT: C  419 MET cc_start: 0.7315 (mtt) cc_final: 0.7011 (ttm)
REVERT: D   63 TRP cc_start: 0.8546 (m100) cc_final: 0.8164 (m100)
REVERT: D  460 THR cc_start: 0.9093 (p) cc_final: 0.8780 (t)
REVERT: D  465 ASN cc_start: 0.8115 (p0) cc_final: 0.7754 (p0)
  outliers start: 14
  outliers final: 6
  residues processed: 110
  average time/residue: 0.0724
  time to fit residues: 11.5480
Evaluate side-chains
  96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.158799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.122479 restraints weight = 12556.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.48
r_work: 0.3475 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8469  Z= 0.117
  Angle     :  0.500   5.859  11869  Z= 0.252
  Chirality :  0.036   0.177   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 18.677 110.315   2116
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.84 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.31), residues: 805
  helix:  1.19 (0.32), residues: 272
  sheet: -0.98 (0.46), residues: 132
  loop : -0.28 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 214 
 TYR   0.010   0.001   TYR D 470 
 PHE   0.014   0.001   PHE B  64 
 TRP   0.008   0.001   TRP D  99 
 HIS   0.002   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8469)
  covalent geometry    : angle       0.50046 (11869)
  hydrogen bonds       : bond        0.03303 (  323)
  hydrogen bonds       : angle       3.90677 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 PHE cc_start: 0.7692 (t80) cc_final: 0.7455 (t80)
REVERT: A  205 GLN cc_start: 0.6569 (tm-30) cc_final: 0.6077 (tm-30)
REVERT: B   59 GLN cc_start: 0.8167 (mp10) cc_final: 0.7618 (mp10)
REVERT: B   65 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7864 (tt)
REVERT: B  152 TYR cc_start: 0.8034 (m-80) cc_final: 0.7768 (m-80)
REVERT: C   44 MET cc_start: 0.7820 (tpp) cc_final: 0.7391 (tpt)
REVERT: C  348 TYR cc_start: 0.7567 (t80) cc_final: 0.6906 (t80)
REVERT: C  413 ASN cc_start: 0.7852 (m-40) cc_final: 0.7583 (m110)
REVERT: C  419 MET cc_start: 0.7237 (mtt) cc_final: 0.6871 (ttm)
REVERT: D   63 TRP cc_start: 0.8511 (m100) cc_final: 0.8116 (m100)
REVERT: D  460 THR cc_start: 0.9062 (p) cc_final: 0.8777 (t)
REVERT: D  465 ASN cc_start: 0.8136 (p0) cc_final: 0.7745 (p0)
REVERT: D  509 ASP cc_start: 0.8082 (t0) cc_final: 0.7848 (t70)
  outliers start: 9
  outliers final: 4
  residues processed: 102
  average time/residue: 0.0697
  time to fit residues: 10.2745
Evaluate side-chains
  96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 22 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 86 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.156948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.120253 restraints weight = 12703.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.39
r_work: 0.3445 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8469  Z= 0.167
  Angle     :  0.533   5.690  11869  Z= 0.270
  Chirality :  0.038   0.179   1384
  Planarity :  0.004   0.048   1229
  Dihedral  : 18.675 110.253   2116
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.11 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.31), residues: 805
  helix:  1.13 (0.31), residues: 272
  sheet: -0.93 (0.46), residues: 132
  loop : -0.30 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 214 
 TYR   0.015   0.001   TYR D 470 
 PHE   0.010   0.001   PHE A 244 
 TRP   0.007   0.001   TRP D  82 
 HIS   0.002   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 8469)
  covalent geometry    : angle       0.53262 (11869)
  hydrogen bonds       : bond        0.03562 (  323)
  hydrogen bonds       : angle       4.01592 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 GLN cc_start: 0.8176 (mp10) cc_final: 0.7582 (mp10)
REVERT: B   65 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7873 (tt)
REVERT: C   44 MET cc_start: 0.7779 (tpp) cc_final: 0.7428 (tpt)
REVERT: C  348 TYR cc_start: 0.7710 (t80) cc_final: 0.7017 (t80)
REVERT: C  419 MET cc_start: 0.7363 (mtt) cc_final: 0.6999 (ttm)
REVERT: D  460 THR cc_start: 0.9075 (p) cc_final: 0.8795 (t)
REVERT: D  465 ASN cc_start: 0.8158 (p0) cc_final: 0.7762 (p0)
  outliers start: 15
  outliers final: 9
  residues processed: 108
  average time/residue: 0.0676
  time to fit residues: 10.8284
Evaluate side-chains
  96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  133 LEU
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0000
   chunk 8 optimal weight:   20.0000
   chunk 27 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN
C 413 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.159025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.120062 restraints weight = 12521.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.39
r_work: 0.3484 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8469  Z= 0.118
  Angle     :  0.508   6.247  11869  Z= 0.257
  Chirality :  0.037   0.183   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 18.660 109.461   2116
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.84 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.31), residues: 805
  helix:  1.20 (0.32), residues: 274
  sheet: -0.70 (0.47), residues: 130
  loop : -0.27 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 193 
 TYR   0.014   0.001   TYR D 470 
 PHE   0.021   0.001   PHE B  64 
 TRP   0.033   0.001   TRP D  63 
 HIS   0.002   0.000   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8469)
  covalent geometry    : angle       0.50830 (11869)
  hydrogen bonds       : bond        0.03280 (  323)
  hydrogen bonds       : angle       3.86805 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 GLN cc_start: 0.6609 (tm-30) cc_final: 0.6187 (tm-30)
REVERT: B   40 MET cc_start: 0.6146 (mtp) cc_final: 0.5836 (mtp)
REVERT: B   59 GLN cc_start: 0.8149 (mp10) cc_final: 0.7592 (mp10)
REVERT: C   44 MET cc_start: 0.7753 (tpp) cc_final: 0.7258 (tpt)
REVERT: C  348 TYR cc_start: 0.7437 (t80) cc_final: 0.6795 (t80)
REVERT: C  413 ASN cc_start: 0.7923 (m-40) cc_final: 0.7640 (m110)
REVERT: D   63 TRP cc_start: 0.8434 (m100) cc_final: 0.8204 (m100)
REVERT: D  460 THR cc_start: 0.9018 (p) cc_final: 0.8765 (t)
REVERT: D  465 ASN cc_start: 0.8130 (p0) cc_final: 0.7739 (p0)
  outliers start: 12
  outliers final: 6
  residues processed: 105
  average time/residue: 0.0714
  time to fit residues: 10.8015
Evaluate side-chains
  93 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0670
   chunk 68 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.9122

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.158431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.121009 restraints weight = 12561.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.41
r_work: 0.3469 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8469  Z= 0.146
  Angle     :  0.531   7.180  11869  Z= 0.266
  Chirality :  0.037   0.179   1384
  Planarity :  0.004   0.048   1229
  Dihedral  : 18.634 108.972   2116
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.28 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.31), residues: 805
  helix:  1.12 (0.31), residues: 275
  sheet: -0.78 (0.47), residues: 132
  loop : -0.31 (0.34), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 193 
 TYR   0.013   0.001   TYR D 470 
 PHE   0.013   0.001   PHE A 233 
 TRP   0.022   0.001   TRP D  63 
 HIS   0.002   0.000   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8469)
  covalent geometry    : angle       0.53123 (11869)
  hydrogen bonds       : bond        0.03448 (  323)
  hydrogen bonds       : angle       3.93518 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 GLN cc_start: 0.6630 (tm-30) cc_final: 0.6156 (tm-30)
REVERT: B   40 MET cc_start: 0.6187 (mtp) cc_final: 0.5872 (mtp)
REVERT: B   49 MET cc_start: 0.5559 (tpp) cc_final: 0.5255 (ttm)
REVERT: B   59 GLN cc_start: 0.8140 (mp10) cc_final: 0.7569 (mp10)
REVERT: B   64 PHE cc_start: 0.8258 (t80) cc_final: 0.8007 (t80)
REVERT: C   44 MET cc_start: 0.7840 (tpp) cc_final: 0.7459 (tpt)
REVERT: C  348 TYR cc_start: 0.7224 (t80) cc_final: 0.6727 (t80)
REVERT: C  413 ASN cc_start: 0.7987 (m-40) cc_final: 0.7705 (m110)
REVERT: D   63 TRP cc_start: 0.8493 (m100) cc_final: 0.8223 (m100)
REVERT: D  460 THR cc_start: 0.8999 (p) cc_final: 0.8757 (t)
REVERT: D  465 ASN cc_start: 0.8170 (p0) cc_final: 0.7768 (p0)
  outliers start: 11
  outliers final: 9
  residues processed: 100
  average time/residue: 0.0757
  time to fit residues: 10.8027
Evaluate side-chains
  100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  395 LEU
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 74 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0470
   chunk 78 optimal weight:    0.0870
   chunk 50 optimal weight:    0.0070
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.2674

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.162971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.125817 restraints weight = 12634.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.41
r_work: 0.3540 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8469  Z= 0.091
  Angle     :  0.485   6.307  11869  Z= 0.244
  Chirality :  0.036   0.181   1384
  Planarity :  0.004   0.046   1229
  Dihedral  : 18.581 106.695   2116
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 18.01 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.31), residues: 805
  helix:  1.31 (0.32), residues: 274
  sheet: -0.60 (0.47), residues: 132
  loop : -0.30 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 193 
 TYR   0.013   0.001   TYR D 470 
 PHE   0.013   0.001   PHE A 233 
 TRP   0.019   0.001   TRP D  63 
 HIS   0.002   0.000   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 8469)
  covalent geometry    : angle       0.48458 (11869)
  hydrogen bonds       : bond        0.03097 (  323)
  hydrogen bonds       : angle       3.66764 (  809)

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

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

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1610 Ramachandran restraints generated.
    805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 GLN cc_start: 0.6666 (tm-30) cc_final: 0.6301 (tm-30)
REVERT: B   59 GLN cc_start: 0.8102 (mp10) cc_final: 0.7594 (mp10)
REVERT: B   64 PHE cc_start: 0.8183 (t80) cc_final: 0.7981 (t80)
REVERT: B  152 TYR cc_start: 0.7830 (m-80) cc_final: 0.7377 (m-80)
REVERT: C   44 MET cc_start: 0.7851 (tpp) cc_final: 0.7280 (tpt)
REVERT: C  348 TYR cc_start: 0.6886 (t80) cc_final: 0.6523 (t80)
REVERT: C  413 ASN cc_start: 0.7821 (m-40) cc_final: 0.7580 (m110)
REVERT: D   63 TRP cc_start: 0.8476 (m100) cc_final: 0.8206 (m100)
REVERT: D  465 ASN cc_start: 0.8114 (p0) cc_final: 0.7731 (p0)
REVERT: D  509 ASP cc_start: 0.8072 (t0) cc_final: 0.7797 (t70)
  outliers start: 7
  outliers final: 5
  residues processed: 108
  average time/residue: 0.0696
  time to fit residues: 10.8658
Evaluate side-chains
  94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain C residue  387 VAL
Chi-restraints excluded: chain C residue  454 VAL
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  150 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 18 optimal weight:    0.4980
   chunk 66 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 GLN
C  47 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.160031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.122154 restraints weight = 12621.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.48
r_work: 0.3487 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8469  Z= 0.127
  Angle     :  0.517   6.599  11869  Z= 0.262
  Chirality :  0.037   0.175   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 18.508 106.580   2116
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.86 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.31), residues: 805
  helix:  1.18 (0.31), residues: 280
  sheet: -0.56 (0.47), residues: 132
  loop : -0.31 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 193 
 TYR   0.015   0.001   TYR D 155 
 PHE   0.012   0.001   PHE A 233 
 TRP   0.012   0.001   TRP D  63 
 HIS   0.002   0.000   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8469)
  covalent geometry    : angle       0.51674 (11869)
  hydrogen bonds       : bond        0.03220 (  323)
  hydrogen bonds       : angle       3.77705 (  809)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1791.44 seconds
wall clock time: 31 minutes 21.30 seconds (1881.30 seconds total)