Starting phenix.real_space_refine
on Thu Jul  2 10:38:21 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7uxa_26856/07_2026/7uxa_26856.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uxa_26856/07_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7uxa_26856/07_2026/7uxa_26856.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7uxa_26856/07_2026/7uxa_26856.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uxa_26856/07_2026/7uxa_26856.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uxa_26856/07_2026/7uxa_26856.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uxa_26856/07_2026/7uxa_26856.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uxa_26856/07_2026/7uxa_26856.cif"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 1.88, per 1000 atoms: 0.23
  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: 0.81
  Conformation dependent library (CDL) restraints added in 476.0 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: 0.87
  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: 1.31

  Time building geometry restraints manager: 1.04 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: 4722
       24.49 -    48.98: 135
       48.98 -    73.47: 25
       73.47 -    97.97: 5
       97.97 -   122.46: 3
  Dihedral angle restraints: 4890
    sinusoidal: 2517
      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 4887 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:             2.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.350
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
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  : 11.946 122.458   3360
  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/Z
  covalent geometry    : bond        0.00341 /  0.17 ( 8469)
  covalent geometry    : angle       0.57696 /  0.33 (11869)
  hydrogen bonds       : bond        0.14263 /  9.78 (  323)
  hydrogen bonds       : angle       5.92833 /  4.12 (  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  : 0.278 
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: 0.0875
  time to fit residues: 19.0815
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  : 0.273 
-------------------------------------------------------------------------------
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...
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 = 0.4212 r_free = 0.4212 target = 0.166545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.128352 restraints weight = 12639.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.32
r_work: 0.3583 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8469  Z= 0.144
  Angle     :  0.533   5.526  11869  Z= 0.273
  Chirality :  0.038   0.168   1384
  Planarity :  0.004   0.050   1229
  Dihedral  : 11.347 118.747   1833
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.27 %
    Favored  : 87.26 %
  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:  0.70 (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 B  64 
 TRP   0.011   0.001   TRP D  99 
 HIS   0.003   0.001   HIS B 116 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 ( 8469)
  covalent geometry    : angle       0.53295 /  0.27 (11869)
  hydrogen bonds       : bond        0.03944 /  2.64 (  323)
  hydrogen bonds       : angle       4.39631 /  3.09 (  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  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   44 MET cc_start: 0.7812 (tpp) cc_final: 0.7491 (tpt)
REVERT: C   58 GLU cc_start: 0.5883 (mt-10) cc_final: 0.5043 (tp30)
REVERT: C  348 TYR cc_start: 0.7053 (t80) cc_final: 0.6704 (t80)
REVERT: C  413 ASN cc_start: 0.7947 (m-40) cc_final: 0.7709 (m110)
REVERT: C  429 MET cc_start: 0.6038 (tmm) cc_final: 0.5800 (tmm)
REVERT: D  460 THR cc_start: 0.9123 (p) cc_final: 0.8757 (t)
REVERT: D  465 ASN cc_start: 0.7824 (p0) cc_final: 0.7532 (p0)
REVERT: D  509 ASP cc_start: 0.8133 (t0) cc_final: 0.7841 (t70)
  outliers start: 10
  outliers final: 5
  residues processed: 121
  average time/residue: 0.0753
  time to fit residues: 12.4132
Evaluate side-chains
  107 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0770
   chunk 16 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4215 r_free = 0.4215 target = 0.166941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.128886 restraints weight = 12366.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.31
r_work: 0.3589 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2277

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= 0.123
  Angle     :  0.522   6.155  11869  Z= 0.267
  Chirality :  0.037   0.172   1384
  Planarity :  0.004   0.050   1229
  Dihedral  : 11.097 118.244   1828
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.62 %
    Favored  : 84.77 %
  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: -0.27 (0.31), residues: 805
  helix:  0.88 (0.31), residues: 272
  sheet: -1.38 (0.45), residues: 134
  loop : -0.38 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 214 
 TYR   0.015   0.001   TYR B  67 
 PHE   0.012   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/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 8469)
  covalent geometry    : angle       0.52200 /  0.27 (11869)
  hydrogen bonds       : bond        0.03568 /  2.38 (  323)
  hydrogen bonds       : angle       4.11816 /  2.91 (  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
  121 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 GLN cc_start: 0.8026 (mp10) cc_final: 0.7775 (mp10)
REVERT: C   44 MET cc_start: 0.7837 (tpp) cc_final: 0.7546 (tpt)
REVERT: C  348 TYR cc_start: 0.7523 (t80) cc_final: 0.6839 (t80)
REVERT: C  413 ASN cc_start: 0.7873 (m-40) cc_final: 0.7652 (m110)
REVERT: C  429 MET cc_start: 0.5965 (tmm) cc_final: 0.5740 (tmm)
REVERT: D   63 TRP cc_start: 0.8533 (m100) cc_final: 0.8186 (m100)
REVERT: D  155 TYR cc_start: 0.8590 (t80) cc_final: 0.8347 (t80)
REVERT: D  460 THR cc_start: 0.9103 (p) cc_final: 0.8749 (t)
REVERT: D  465 ASN cc_start: 0.7955 (p0) cc_final: 0.7669 (p0)
  outliers start: 11
  outliers final: 4
  residues processed: 117
  average time/residue: 0.0809
  time to fit residues: 13.2075
Evaluate side-chains
  103 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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  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:    0.9980
   chunk 24 optimal weight:    0.0040
   chunk 43 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.1396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 ASN
A  78 HIS
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.164836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.126406 restraints weight = 12715.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.32
r_work: 0.3554 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2571

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= 0.169
  Angle     :  0.541   5.664  11869  Z= 0.275
  Chirality :  0.038   0.173   1384
  Planarity :  0.004   0.049   1229
  Dihedral  : 11.167 115.203   1828
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.20 %
    Favored  : 84.19 %
  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: -0.23 (0.31), residues: 805
  helix:  0.98 (0.31), residues: 270
  sheet: -1.37 (0.45), residues: 134
  loop : -0.40 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 340 
 TYR   0.014   0.002   TYR D 155 
 PHE   0.013   0.002   PHE A 233 
 TRP   0.008   0.001   TRP D  99 
 HIS   0.002   0.001   HIS A  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.17 ( 8469)
  covalent geometry    : angle       0.54112 /  0.28 (11869)
  hydrogen bonds       : bond        0.03749 /  2.52 (  323)
  hydrogen bonds       : angle       4.20984 /  2.97 (  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
  117 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.239 
Fit side-chains
REVERT: B   40 MET cc_start: 0.5699 (mtp) cc_final: 0.5357 (mtp)
REVERT: B   59 GLN cc_start: 0.8073 (mp10) cc_final: 0.7620 (mp10)
REVERT: B   68 LEU cc_start: 0.8675 (mt) cc_final: 0.8263 (mm)
REVERT: C   44 MET cc_start: 0.7732 (tpp) cc_final: 0.7443 (tpt)
REVERT: C   68 LYS cc_start: 0.6712 (tttt) cc_final: 0.6222 (ttpp)
REVERT: C  348 TYR cc_start: 0.7693 (t80) cc_final: 0.6975 (t80)
REVERT: C  413 ASN cc_start: 0.7902 (m-40) cc_final: 0.7651 (m110)
REVERT: C  419 MET cc_start: 0.7398 (mtt) cc_final: 0.6829 (mtp)
REVERT: D   63 TRP cc_start: 0.8512 (m100) cc_final: 0.8228 (m100)
REVERT: D  460 THR cc_start: 0.9101 (p) cc_final: 0.8758 (t)
REVERT: D  465 ASN cc_start: 0.8000 (p0) cc_final: 0.7670 (p0)
  outliers start: 11
  outliers final: 6
  residues processed: 112
  average time/residue: 0.0757
  time to fit residues: 11.8933
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  : 0.158 
-------------------------------------------------------------------------------
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  395 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.0050
   chunk 63 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 85 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.6596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4114 r_free = 0.4114 target = 0.158414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.119385 restraints weight = 12654.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.41
r_work: 0.3473 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8469  Z= 0.120
  Angle     :  0.510   5.817  11869  Z= 0.259
  Chirality :  0.037   0.175   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 11.049 113.279   1828
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.67 %
    Favored  : 82.72 %
  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: -0.01 (0.31), residues: 805
  helix:  1.15 (0.32), residues: 270
  sheet: -1.09 (0.46), residues: 132
  loop : -0.33 (0.34), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 214 
 TYR   0.013   0.001   TYR D 470 
 PHE   0.016   0.001   PHE A  94 
 TRP   0.010   0.001   TRP C 354 
 HIS   0.002   0.001   HIS B 116 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 8469)
  covalent geometry    : angle       0.51042 /  0.26 (11869)
  hydrogen bonds       : bond        0.03414 /  2.28 (  323)
  hydrogen bonds       : angle       3.98786 /  2.83 (  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
  110 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: B   40 MET cc_start: 0.5636 (mtp) cc_final: 0.5309 (mtp)
REVERT: B   59 GLN cc_start: 0.8093 (mp10) cc_final: 0.7564 (mp10)
REVERT: C   44 MET cc_start: 0.7846 (tpp) cc_final: 0.7412 (tpt)
REVERT: C   68 LYS cc_start: 0.6377 (tttt) cc_final: 0.6133 (ttpp)
REVERT: C  305 PHE cc_start: 0.7997 (t80) cc_final: 0.7789 (t80)
REVERT: C  348 TYR cc_start: 0.7695 (t80) cc_final: 0.6901 (t80)
REVERT: C  413 ASN cc_start: 0.7840 (m-40) cc_final: 0.7587 (m110)
REVERT: C  419 MET cc_start: 0.7305 (mtt) cc_final: 0.6843 (mtp)
REVERT: D   63 TRP cc_start: 0.8530 (m100) cc_final: 0.8180 (m100)
REVERT: D  460 THR cc_start: 0.9060 (p) cc_final: 0.8750 (t)
REVERT: D  465 ASN cc_start: 0.8108 (p0) cc_final: 0.7727 (p0)
  outliers start: 11
  outliers final: 5
  residues processed: 108
  average time/residue: 0.0701
  time to fit residues: 11.1923
Evaluate side-chains
  95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
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  150 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0170
   chunk 7 optimal weight:    0.0370
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.4096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN
D 522 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.160428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.121662 restraints weight = 12545.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.40
r_work: 0.3505 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8469  Z= 0.098
  Angle     :  0.487   5.895  11869  Z= 0.247
  Chirality :  0.036   0.172   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 10.862 110.588   1828
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.84 %
    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:  0.07 (0.31), residues: 805
  helix:  1.18 (0.32), residues: 277
  sheet: -0.93 (0.47), residues: 130
  loop : -0.34 (0.34), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 340 
 TYR   0.010   0.001   TYR D 470 
 PHE   0.012   0.001   PHE A  94 
 TRP   0.008   0.001   TRP D  99 
 HIS   0.002   0.000   HIS B 116 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.10 ( 8469)
  covalent geometry    : angle       0.48688 /  0.25 (11869)
  hydrogen bonds       : bond        0.03189 /  2.10 (  323)
  hydrogen bonds       : angle       3.76280 /  2.68 (  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: 10
    poor density    : 95
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  205 GLN cc_start: 0.6556 (tm-30) cc_final: 0.6149 (tm-30)
REVERT: B   40 MET cc_start: 0.5834 (mtp) cc_final: 0.5549 (mtp)
REVERT: B   59 GLN cc_start: 0.8130 (mp10) cc_final: 0.7613 (mp10)
REVERT: B   65 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7982 (tt)
REVERT: B  149 THR cc_start: 0.8475 (p) cc_final: 0.8256 (p)
REVERT: B  152 TYR cc_start: 0.7830 (m-80) cc_final: 0.7411 (m-80)
REVERT: C   44 MET cc_start: 0.7943 (tpp) cc_final: 0.7448 (tpt)
REVERT: C  348 TYR cc_start: 0.7619 (t80) cc_final: 0.6873 (t80)
REVERT: C  354 TRP cc_start: 0.7376 (m100) cc_final: 0.6733 (m100)
REVERT: C  413 ASN cc_start: 0.7851 (m-40) cc_final: 0.7592 (m110)
REVERT: C  419 MET cc_start: 0.7255 (mtt) cc_final: 0.6785 (mtp)
REVERT: D   63 TRP cc_start: 0.8521 (m100) cc_final: 0.8137 (m100)
REVERT: D  460 THR cc_start: 0.9019 (p) cc_final: 0.8746 (t)
REVERT: D  465 ASN cc_start: 0.8139 (p0) cc_final: 0.7746 (p0)
  outliers start: 10
  outliers final: 5
  residues processed: 103
  average time/residue: 0.0724
  time to fit residues: 10.9417
Evaluate side-chains
  94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
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  454 VAL
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  519 THR
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:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0970
   chunk 0 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 522 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.156235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.116450 restraints weight = 12653.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.49
r_work: 0.3425 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8469  Z= 0.199
  Angle     :  0.556   5.679  11869  Z= 0.281
  Chirality :  0.038   0.174   1384
  Planarity :  0.004   0.048   1229
  Dihedral  : 11.124 110.916   1828
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.69 %
    Favored  : 81.99 %
  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: -0.15 (0.31), residues: 805
  helix:  0.96 (0.31), residues: 278
  sheet: -1.03 (0.46), residues: 132
  loop : -0.44 (0.34), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 193 
 TYR   0.022   0.002   TYR D 155 
 PHE   0.011   0.002   PHE A 244 
 TRP   0.008   0.001   TRP D  82 
 HIS   0.002   0.001   HIS A 211 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00456 /  0.20 ( 8469)
  covalent geometry    : angle       0.55589 /  0.28 (11869)
  hydrogen bonds       : bond        0.03731 /  2.51 (  323)
  hydrogen bonds       : angle       4.09183 /  2.90 (  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
  106 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 PHE cc_start: 0.7612 (t80) cc_final: 0.7348 (t80)
REVERT: B   40 MET cc_start: 0.5979 (mtp) cc_final: 0.5609 (mtp)
REVERT: B   59 GLN cc_start: 0.8142 (mp10) cc_final: 0.7587 (mp10)
REVERT: B   65 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7870 (tt)
REVERT: B  152 TYR cc_start: 0.8163 (m-80) cc_final: 0.7961 (m-80)
REVERT: C   44 MET cc_start: 0.7919 (tpp) cc_final: 0.7600 (tpt)
REVERT: C   47 ASN cc_start: 0.7345 (p0) cc_final: 0.7029 (p0)
REVERT: C  348 TYR cc_start: 0.7793 (t80) cc_final: 0.6986 (t80)
REVERT: C  419 MET cc_start: 0.7422 (mtt) cc_final: 0.6962 (mtp)
REVERT: D  460 THR cc_start: 0.9072 (p) cc_final: 0.8790 (t)
REVERT: D  465 ASN cc_start: 0.8152 (p0) cc_final: 0.7753 (p0)
  outliers start: 9
  outliers final: 6
  residues processed: 106
  average time/residue: 0.0722
  time to fit residues: 11.3787
Evaluate side-chains
  99 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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  454 VAL
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:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 8 optimal weight:   20.0000
   chunk 27 optimal weight:    7.9990
   chunk 87 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A   8 ASN
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.158652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.119508 restraints weight = 12478.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.44
r_work: 0.3458 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8469  Z= 0.123
  Angle     :  0.510   5.779  11869  Z= 0.259
  Chirality :  0.037   0.179   1384
  Planarity :  0.004   0.048   1229
  Dihedral  : 11.002 110.610   1828
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 17.72 %
    Favored  : 80.82 %
  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: -0.01 (0.31), residues: 805
  helix:  1.08 (0.31), residues: 280
  sheet: -0.89 (0.46), residues: 130
  loop : -0.41 (0.34), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 193 
 TYR   0.016   0.001   TYR D 470 
 PHE   0.015   0.001   PHE A 233 
 TRP   0.033   0.001   TRP D  63 
 HIS   0.002   0.001   HIS D 431 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.12 ( 8469)
  covalent geometry    : angle       0.51025 /  0.26 (11869)
  hydrogen bonds       : bond        0.03306 /  2.20 (  323)
  hydrogen bonds       : angle       3.90137 /  2.77 (  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
  101 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 PHE cc_start: 0.7667 (t80) cc_final: 0.7380 (t80)
REVERT: B   40 MET cc_start: 0.5904 (mtp) cc_final: 0.5549 (mtp)
REVERT: B   59 GLN cc_start: 0.8139 (mp10) cc_final: 0.7585 (mp10)
REVERT: B   65 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7853 (tt)
REVERT: B  152 TYR cc_start: 0.8012 (m-80) cc_final: 0.7509 (m-80)
REVERT: C   44 MET cc_start: 0.7881 (tpp) cc_final: 0.7452 (tpt)
REVERT: C   47 ASN cc_start: 0.7378 (p0) cc_final: 0.7127 (p0)
REVERT: C  348 TYR cc_start: 0.7714 (t80) cc_final: 0.6891 (t80)
REVERT: C  354 TRP cc_start: 0.7239 (m100) cc_final: 0.6548 (m100)
REVERT: C  413 ASN cc_start: 0.7978 (m110) cc_final: 0.7507 (m110)
REVERT: D   63 TRP cc_start: 0.8423 (m100) cc_final: 0.8214 (m100)
REVERT: D  155 TYR cc_start: 0.8584 (t80) cc_final: 0.8372 (t80)
REVERT: D  460 THR cc_start: 0.9023 (p) cc_final: 0.8779 (t)
REVERT: D  465 ASN cc_start: 0.8152 (p0) cc_final: 0.7747 (p0)
  outliers start: 10
  outliers final: 7
  residues processed: 100
  average time/residue: 0.0797
  time to fit residues: 11.6433
Evaluate side-chains
  96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  115 SER
Chi-restraints excluded: chain C residue  308 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    0.1980
   chunk 68 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.158110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.121073 restraints weight = 12495.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.53
r_work: 0.3455 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8469  Z= 0.142
  Angle     :  0.526   5.773  11869  Z= 0.266
  Chirality :  0.037   0.178   1384
  Planarity :  0.004   0.048   1229
  Dihedral  : 11.002 110.179   1828
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.16 %
    Favored  : 80.38 %
  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: -0.07 (0.31), residues: 805
  helix:  1.06 (0.31), residues: 280
  sheet: -0.92 (0.46), residues: 132
  loop : -0.46 (0.33), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 193 
 TYR   0.015   0.001   TYR D 470 
 PHE   0.013   0.001   PHE A 233 
 TRP   0.023   0.001   TRP D  63 
 HIS   0.002   0.001   HIS A 211 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 8469)
  covalent geometry    : angle       0.52550 /  0.27 (11869)
  hydrogen bonds       : bond        0.03366 /  2.25 (  323)
  hydrogen bonds       : angle       3.93504 /  2.80 (  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
  97 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 MET cc_start: 0.5915 (mtp) cc_final: 0.5577 (mtp)
REVERT: B   49 MET cc_start: 0.5675 (tpp) cc_final: 0.5469 (ttm)
REVERT: B   59 GLN cc_start: 0.8139 (mp10) cc_final: 0.7580 (mp10)
REVERT: B   65 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7853 (tt)
REVERT: B  132 ASP cc_start: 0.8109 (t0) cc_final: 0.7707 (t0)
REVERT: B  152 TYR cc_start: 0.8090 (m-80) cc_final: 0.7886 (m-80)
REVERT: C   44 MET cc_start: 0.7875 (tpp) cc_final: 0.7447 (tpt)
REVERT: C   47 ASN cc_start: 0.7391 (p0) cc_final: 0.7148 (p0)
REVERT: C  348 TYR cc_start: 0.7682 (t80) cc_final: 0.6898 (t80)
REVERT: C  354 TRP cc_start: 0.7089 (m100) cc_final: 0.6410 (m100)
REVERT: C  413 ASN cc_start: 0.7998 (m110) cc_final: 0.7519 (m110)
REVERT: D   63 TRP cc_start: 0.8491 (m100) cc_final: 0.8237 (m100)
REVERT: D  460 THR cc_start: 0.9021 (p) cc_final: 0.8767 (t)
REVERT: D  465 ASN cc_start: 0.8180 (p0) cc_final: 0.7776 (p0)
  outliers start: 10
  outliers final: 8
  residues processed: 96
  average time/residue: 0.0725
  time to fit residues: 10.3451
Evaluate side-chains
  95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
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  105 VAL
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain C residue  308 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0670
   chunk 74 optimal weight:    0.7980
   chunk 35 optimal weight:    0.2980
   chunk 78 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.5518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.159260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.121714 restraints weight = 12510.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.40
r_work: 0.3495 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8469  Z= 0.109
  Angle     :  0.497   6.252  11869  Z= 0.251
  Chirality :  0.036   0.179   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 10.843 108.530   1828
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 18.59 %
    Favored  : 80.23 %
  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:  0.11 (0.31), residues: 805
  helix:  1.21 (0.32), residues: 280
  sheet: -0.70 (0.46), residues: 130
  loop : -0.41 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 193 
 TYR   0.014   0.001   TYR D 470 
 PHE   0.013   0.001   PHE A 233 
 TRP   0.019   0.001   TRP D  63 
 HIS   0.001   0.000   HIS B  77 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 8469)
  covalent geometry    : angle       0.49665 /  0.25 (11869)
  hydrogen bonds       : bond        0.03140 /  2.08 (  323)
  hydrogen bonds       : angle       3.78257 /  2.70 (  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
  95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 MET cc_start: 0.5875 (mtp) cc_final: 0.5488 (mtp)
REVERT: B   59 GLN cc_start: 0.8099 (mp10) cc_final: 0.7550 (mp10)
REVERT: B   65 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7812 (tt)
REVERT: B  132 ASP cc_start: 0.8133 (t0) cc_final: 0.7734 (t0)
REVERT: B  152 TYR cc_start: 0.8012 (m-80) cc_final: 0.7543 (m-80)
REVERT: C   44 MET cc_start: 0.7938 (tpp) cc_final: 0.7415 (tpt)
REVERT: C   47 ASN cc_start: 0.7424 (p0) cc_final: 0.7203 (p0)
REVERT: C  348 TYR cc_start: 0.7620 (t80) cc_final: 0.6864 (t80)
REVERT: C  354 TRP cc_start: 0.6951 (m100) cc_final: 0.6262 (m100)
REVERT: C  413 ASN cc_start: 0.7995 (m110) cc_final: 0.7508 (m110)
REVERT: D   63 TRP cc_start: 0.8487 (m100) cc_final: 0.8238 (m100)
REVERT: D  155 TYR cc_start: 0.8561 (t80) cc_final: 0.8336 (t80)
REVERT: D  460 THR cc_start: 0.8961 (p) cc_final: 0.8741 (t)
REVERT: D  465 ASN cc_start: 0.8148 (p0) cc_final: 0.7759 (p0)
REVERT: D  509 ASP cc_start: 0.8018 (t0) cc_final: 0.7803 (t70)
  outliers start: 8
  outliers final: 7
  residues processed: 94
  average time/residue: 0.0761
  time to fit residues: 10.6134
Evaluate side-chains
  92 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   90 ILE
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  454 VAL
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:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 87 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.159170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.122103 restraints weight = 12580.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.51
r_work: 0.3471 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3223

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= 0.131
  Angle     :  0.506   6.344  11869  Z= 0.255
  Chirality :  0.037   0.176   1384
  Planarity :  0.004   0.047   1229
  Dihedral  : 10.850 107.877   1828
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 18.16 %
    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:  0.05 (0.31), residues: 805
  helix:  1.17 (0.31), residues: 280
  sheet: -0.77 (0.46), residues: 132
  loop : -0.43 (0.33), residues: 393

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   0.015   0.001   PHE A 233 
 TRP   0.016   0.001   TRP D  63 
 HIS   0.002   0.000   HIS A 211 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.13 ( 8469)
  covalent geometry    : angle       0.50575 /  0.25 (11869)
  hydrogen bonds       : bond        0.03228 /  2.15 (  323)
  hydrogen bonds       : angle       3.85521 /  2.74 (  809)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1810.07 seconds
wall clock time: 31 minutes 45.84 seconds (1905.84 seconds total)