Starting phenix.real_space_refine
on Sat Sep 12 06:39:10 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7xpx_33385/09_2026/7xpx_33385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xpx_33385/09_2026/7xpx_33385.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xpx_33385/09_2026/7xpx_33385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xpx_33385/09_2026/7xpx_33385.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7xpx_33385/09_2026/7xpx_33385.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7xpx_33385/09_2026/7xpx_33385.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xpx_33385/09_2026/7xpx_33385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xpx_33385/09_2026/7xpx_33385.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1341 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      20      5.16       5
     C    7508      2.51       5
     N    2521      2.21       5
     O    3071      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13408
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 820
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 693
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'ECX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 756
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 808
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 757
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "I"
      Number of atoms: 2970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2970
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2969
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 1338
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 167, 1337
          Classifications: {'peptide': 167}
          Link IDs: {'PTRANS': 3, 'TRANS': 163}
      Conformer: "B"
        Number of residues, atoms: 167, 1337
          Classifications: {'peptide': 167}
          Link IDs: {'PTRANS': 3, 'TRANS': 163}
          bond proxies already assigned to first conformer: 1359
    Chain: "K"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Time building chain proxies: 3.43, per 1000 atoms: 0.26
  Number of scatterers: 13408
  At special positions: 0
  Unit cell: (94, 120, 121, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P     288     15.00
     O    3071      8.00
     N    2521      7.00
     C    7508      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: 1.12
  Conformation dependent library (CDL) restraints added in 420.6 milliseconds
  

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1748

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 14 sheets defined
      62.1% alpha, 7.0% beta
      137 base pairs and 257 stacking pairs defined.
    Time for finding SS restraints: 2.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.556A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.265A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.798A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.567A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.289A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 121
    Processing helix  chain 'K' and resid 199 through 208
      removed outlier: 3.720A  pdb=" N   ARG K 205 " --> pdb=" O   GLU K 201 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 251 through 265
      removed outlier: 3.982A  pdb=" N   LYS K 257 " --> pdb=" O   THR K 253 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 340 through 347
      removed outlier: 3.577A  pdb=" N   GLU K 345 " --> pdb=" O   LYS K 341 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA K 346 " --> pdb=" O   ALA K 342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.741A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.559A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.134A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.881A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.477A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 218 through 223
    Processing sheet with id=AB3, first strand: chain 'K' and resid 241 through 245
      removed outlier: 6.934A  pdb=" N   PHE K 241 " --> pdb=" O   ALA K 322 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   ALA K 322 " --> pdb=" O   PHE K 241 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU K 318 " --> pdb=" O   TYR K 245 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'K' and resid 248 through 250
    Processing sheet with id=AB5, first strand: chain 'K' and resid 298 through 299
      removed outlier: 6.611A  pdb=" N   ASN K 298 " --> pdb=" O   TYR K 334 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5

    454 hydrogen bonds defined for protein.
    1329 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      354 hydrogen bonds
      708 hydrogen bond angles
      0 basepair planarities
      137 basepair parallelities
      257 stacking parallelities
  Total time for adding SS restraints: 3.21

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3023
        1.34 -     1.46: 4248
        1.46 -     1.58: 6355
        1.58 -     1.70: 576
        1.70 -     1.82: 35
  Bond restraints: 14237
  Sorted by residual:
  bond pdb=" C3'  DC I  34 "
       pdb=" C2'  DC I  34 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.14e+01
  bond pdb=" C3'  DA J -22 "
       pdb=" C2'  DA J -22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.07e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.72e+00
  bond pdb=" C3'  DC J  19 "
       pdb=" C2'  DC J  19 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.37e+00
  bond pdb=" C3'  DG I  10 "
       pdb=" C2'  DG I  10 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.12e+00
  ... (remaining 14232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 19522
        1.82 -     3.63: 892
        3.63 -     5.45: 34
        5.45 -     7.26: 4
        7.26 -     9.08: 5
  Bond angle restraints: 20457
  Sorted by residual:
  angle pdb=" O4'  DT I -26 "
        pdb=" C4'  DT I -26 "
        pdb=" C3'  DT I -26 "
      ideal   model   delta    sigma   weight residual
     106.00  103.18    2.82 6.00e-01 2.78e+00 2.21e+01
  angle pdb=" N3   DT J -42 "
        pdb=" C4   DT J -42 "
        pdb=" O4   DT J -42 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.03e+01
  angle pdb=" N3   DT I -43 "
        pdb=" C4   DT I -43 "
        pdb=" O4   DT I -43 "
      ideal   model   delta    sigma   weight residual
     119.90  122.54   -2.64 6.00e-01 2.78e+00 1.94e+01
  angle pdb=" N3   DT I -39 "
        pdb=" C4   DT I -39 "
        pdb=" O4   DT I -39 "
      ideal   model   delta    sigma   weight residual
     119.90  122.54   -2.64 6.00e-01 2.78e+00 1.94e+01
  angle pdb=" N3   DT I   9 "
        pdb=" C4   DT I   9 "
        pdb=" O4   DT I   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.54   -2.64 6.00e-01 2.78e+00 1.94e+01
  ... (remaining 20452 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.48: 6390
       35.48 -    70.96: 1417
       70.96 -   106.44: 12
      106.44 -   141.92: 2
      141.92 -   177.40: 3
  Dihedral angle restraints: 7824
    sinusoidal: 5112
      harmonic: 2712
  Sorted by residual:
  dihedral pdb=" C4'  DT J  54 "
           pdb=" C3'  DT J  54 "
           pdb=" O3'  DT J  54 "
           pdb=" P    DC J  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.60  177.40     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT I  54 "
           pdb=" C3'  DT I  54 "
           pdb=" O3'  DT I  54 "
           pdb=" P    DC I  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.82 -176.82     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.40  175.60     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 7821 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1445
       0.037 -    0.073: 633
       0.073 -    0.110: 187
       0.110 -    0.147: 41
       0.147 -    0.183: 7
  Chirality restraints: 2313
  Sorted by residual:
  chirality pdb=" CA  GLU D  90 "
            pdb=" N   GLU D  90 "
            pdb=" C   GLU D  90 "
            pdb=" CB  GLU D  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.39e-01
  chirality pdb=" C2' SAM K 401 "
            pdb=" C1' SAM K 401 "
            pdb=" C3' SAM K 401 "
            pdb=" O2' SAM K 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.57   -0.18 2.00e-01 2.50e+01 8.32e-01
  chirality pdb=" C1' SAM K 401 "
            pdb=" C2' SAM K 401 "
            pdb=" N9  SAM K 401 "
            pdb=" O4' SAM K 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.30    2.47   -0.17 2.00e-01 2.50e+01 7.01e-01
  ... (remaining 2310 not shown)

  Planarity restraints: 1588
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  55 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   ARG B  55 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ARG B  55 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLY B  56 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  47 "    0.027 2.00e-02 2.50e+03   1.19e-02 3.88e+00
        pdb=" N9   DA I  47 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8   DA I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  47 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DA I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I  47 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL K 315 "   -0.029 5.00e-02 4.00e+02   4.40e-02 3.09e+00
        pdb=" N   PRO K 316 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO K 316 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO K 316 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1585 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 922
        2.73 -     3.27: 12385
        3.27 -     3.81: 27071
        3.81 -     4.36: 31892
        4.36 -     4.90: 45811
  Nonbonded interactions: 118081
  Sorted by model distance:
  nonbonded pdb=" O   LYS C  15 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   GLU K 208 "
            pdb=" OG  SER K 212 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OE2 GLU D  68 "
            pdb=" NH2 ARG H  76 "
     model   vdw
     2.270 3.120
  ... (remaining 118076 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 27 through 121)
  selection = (chain 'H' and resid 27 through 121)
}
ncs_group {
  reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72))
  selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.330
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  14237  Z= 0.495
  Angle     :  0.763   9.076  20457  Z= 0.644
  Chirality :  0.044   0.183   2313
  Planarity :  0.005   0.052   1588
  Dihedral  : 27.527 177.402   6076
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.27), residues: 913
  helix:  1.35 (0.21), residues: 572
  sheet: -0.78 (0.81), residues: 38
  loop : -0.77 (0.32), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG K 189 
 TYR   0.019   0.002   TYR K 262 
 PHE   0.013   0.002   PHE G  25 
 TRP   0.003   0.001   TRP K 349 
 HIS   0.007   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00572 /  0.49 (14237)
  covalent geometry    : angle       0.76252 /  0.64 (20457)
  hydrogen bonds       : bond        0.10664 /  7.38 (  808)
  hydrogen bonds       : angle       4.14572 /  2.91 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: C   56 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7310 (tm-30)
REVERT: C   95 LYS cc_start: 0.7621 (tttm) cc_final: 0.7349 (ttmt)
REVERT: D   56 MET cc_start: 0.8281 (tpp) cc_final: 0.8077 (tpp)
REVERT: G   75 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8093 (mttm)
REVERT: K  195 LYS cc_start: 0.7410 (tmmt) cc_final: 0.7204 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1712
  time to fit residues: 26.9194
Evaluate side-chains
  114 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.3980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  24 GLN
D  44 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  92 GLN
E 108 ASN
G 110 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.223491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.136055 restraints weight = 14166.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.96
r_work: 0.2955 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (5 function evaluations)
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.0836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  14237  Z= 0.162
  Angle     :  0.655   7.909  20457  Z= 0.377
  Chirality :  0.045   0.304   2313
  Planarity :  0.005   0.038   1588
  Dihedral  : 30.901 179.837   4212
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  6.14 %
    Favored  : 93.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.27), residues: 913
  helix:  1.74 (0.21), residues: 587
  sheet: -0.82 (0.82), residues: 38
  loop : -0.60 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  35 
 TYR   0.019   0.002   TYR B  88 
 PHE   0.008   0.002   PHE K 275 
 TRP   0.004   0.001   TRP K 349 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.16 (14237)
  covalent geometry    : angle       0.65499 /  0.38 (20457)
  hydrogen bonds       : bond        0.04573 /  3.02 (  808)
  hydrogen bonds       : angle       3.39833 /  2.41 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 117
  time to evaluate  : 0.280 
Fit side-chains
REVERT: B   91 LYS cc_start: 0.8740 (tttm) cc_final: 0.8415 (ttpp)
REVERT: C   56 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: C   95 LYS cc_start: 0.7688 (tttm) cc_final: 0.7139 (ttmt)
REVERT: D   56 MET cc_start: 0.8685 (tpp) cc_final: 0.8440 (tpp)
REVERT: G   73 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8539 (t0)
REVERT: G   75 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7642 (mttm)
REVERT: K  197 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6654 (mt-10)
  outliers start: 5
  outliers final: 3
  residues processed: 117
  average time/residue: 0.1621
  time to fit residues: 25.3385
Evaluate side-chains
  115 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain K residue  204 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 67 optimal weight:    0.8980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
F  93 GLN
G 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.210372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.122209 restraints weight = 14067.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 1.99
r_work: 0.2926 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14237  Z= 0.181
  Angle     :  0.618   7.098  20457  Z= 0.358
  Chirality :  0.044   0.311   2313
  Planarity :  0.004   0.037   1588
  Dihedral  : 30.879 179.679   4212
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.06 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.27), residues: 913
  helix:  1.88 (0.21), residues: 587
  sheet: -0.77 (0.82), residues: 38
  loop : -0.57 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  96 
 TYR   0.012   0.001   TYR K 262 
 PHE   0.010   0.001   PHE G  25 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.007   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.18 (14237)
  covalent geometry    : angle       0.61789 /  0.36 (20457)
  hydrogen bonds       : bond        0.04266 /  2.81 (  808)
  hydrogen bonds       : angle       3.22948 /  2.29 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 LYS cc_start: 0.8751 (tttm) cc_final: 0.8432 (ttpp)
REVERT: B   92 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8295 (ttp80)
REVERT: C   35 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7826 (mtm-85)
REVERT: C   56 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8354 (tm-30)
REVERT: C   95 LYS cc_start: 0.7691 (tttm) cc_final: 0.7147 (ttmt)
REVERT: D   34 TYR cc_start: 0.9192 (m-80) cc_final: 0.8872 (m-80)
REVERT: D   56 MET cc_start: 0.8767 (tpp) cc_final: 0.8508 (tpp)
REVERT: G   73 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8452 (t0)
REVERT: G   75 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7762 (mttm)
REVERT: K  197 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6594 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 128
  average time/residue: 0.1699
  time to fit residues: 28.6036
Evaluate side-chains
  133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 110 optimal weight:    6.9990
   chunk 98 optimal weight:   30.0000
   chunk 35 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 40 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0980
   chunk 64 optimal weight:    0.8980
   chunk 75 optimal weight:    9.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.211211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.123285 restraints weight = 14133.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.96
r_work: 0.2947 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2933
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14237  Z= 0.151
  Angle     :  0.593   7.325  20457  Z= 0.346
  Chirality :  0.043   0.313   2313
  Planarity :  0.004   0.036   1588
  Dihedral  : 30.763 179.538   4212
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.46 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.28), residues: 913
  helix:  2.01 (0.21), residues: 587
  sheet: -0.78 (0.82), residues: 38
  loop : -0.41 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 189 
 TYR   0.011   0.001   TYR K 262 
 PHE   0.007   0.001   PHE K 275 
 TRP   0.002   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.15 (14237)
  covalent geometry    : angle       0.59288 /  0.35 (20457)
  hydrogen bonds       : bond        0.03910 /  2.57 (  808)
  hydrogen bonds       : angle       3.11491 /  2.22 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8222 (ttp80)
REVERT: C   35 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7712 (mtm-85)
REVERT: C   56 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8250 (tm-30)
REVERT: C   95 LYS cc_start: 0.7654 (tttm) cc_final: 0.7147 (ttmt)
REVERT: D   56 MET cc_start: 0.8701 (tpp) cc_final: 0.8475 (tpp)
REVERT: F   90 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7829 (mt)
REVERT: G   73 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8499 (t0)
REVERT: K  197 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6559 (mt-10)
  outliers start: 10
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1798
  time to fit residues: 29.0927
Evaluate side-chains
  129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:   30.0000
   chunk 48 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 95 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 96 optimal weight:   10.0000
   chunk 85 optimal weight:   40.0000
   chunk 72 optimal weight:   30.0000
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.211310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.123235 restraints weight = 14187.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.92
r_work: 0.2943 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14237  Z= 0.157
  Angle     :  0.589   7.325  20457  Z= 0.343
  Chirality :  0.043   0.306   2313
  Planarity :  0.004   0.048   1588
  Dihedral  : 30.710 178.389   4212
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  9.21 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.28), residues: 913
  helix:  2.06 (0.21), residues: 584
  sheet: -0.74 (0.82), residues: 38
  loop : -0.39 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  96 
 TYR   0.011   0.001   TYR K 262 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.000   0.000   TRP K 349 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.16 (14237)
  covalent geometry    : angle       0.58879 /  0.34 (20457)
  hydrogen bonds       : bond        0.03904 /  2.57 (  808)
  hydrogen bonds       : angle       3.07332 /  2.19 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7684 (mtm-85)
REVERT: C   95 LYS cc_start: 0.7688 (tttm) cc_final: 0.7170 (ttmt)
REVERT: D   56 MET cc_start: 0.8706 (tpp) cc_final: 0.8470 (tpp)
REVERT: F   90 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7846 (mt)
REVERT: F   93 GLN cc_start: 0.8551 (mt0) cc_final: 0.8344 (mt0)
REVERT: G   73 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8511 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 123
  average time/residue: 0.1814
  time to fit residues: 29.3002
Evaluate side-chains
  130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 104 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 15 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  60 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.211612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.123392 restraints weight = 14014.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.96
r_work: 0.2957 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14237  Z= 0.144
  Angle     :  0.579   7.350  20457  Z= 0.338
  Chirality :  0.042   0.307   2313
  Planarity :  0.004   0.056   1588
  Dihedral  : 30.678 178.280   4212
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.85 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.28), residues: 913
  helix:  2.13 (0.21), residues: 583
  sheet: -0.74 (0.82), residues: 38
  loop : -0.39 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  96 
 TYR   0.010   0.001   TYR K 262 
 PHE   0.007   0.001   PHE E  67 
 TRP   0.000   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.14 (14237)
  covalent geometry    : angle       0.57857 /  0.34 (20457)
  hydrogen bonds       : bond        0.03818 /  2.52 (  808)
  hydrogen bonds       : angle       3.02708 /  2.16 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7678 (mtm-85)
REVERT: C   56 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8250 (tm-30)
REVERT: C   95 LYS cc_start: 0.7691 (tttm) cc_final: 0.7174 (ttmt)
REVERT: D   56 MET cc_start: 0.8724 (tpp) cc_final: 0.8468 (tpp)
REVERT: F   90 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7830 (mt)
REVERT: G   73 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8523 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 118
  average time/residue: 0.1655
  time to fit residues: 25.9889
Evaluate side-chains
  121 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 75 optimal weight:   11.9990
   chunk 46 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 112 optimal weight:    9.9990
   chunk 50 optimal weight:    0.7980
   chunk 94 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   overall best weight:    1.4382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  18 HIS
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.216035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.126644 restraints weight = 14101.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.99
r_work: 0.2896 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2879 r_free = 0.2879    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  14237  Z= 0.211
  Angle     :  0.623  16.107  20457  Z= 0.353
  Chirality :  0.043   0.302   2313
  Planarity :  0.004   0.066   1588
  Dihedral  : 30.727 177.494   4212
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 10.10 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.27), residues: 913
  helix:  1.95 (0.21), residues: 583
  sheet: -0.72 (0.82), residues: 38
  loop : -0.42 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  72 
 TYR   0.012   0.001   TYR G  57 
 PHE   0.010   0.002   PHE G  25 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.21 (14237)
  covalent geometry    : angle       0.62317 /  0.35 (20457)
  hydrogen bonds       : bond        0.04078 /  2.69 (  808)
  hydrogen bonds       : angle       3.14362 /  2.24 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7722 (mtm-85)
REVERT: C   95 LYS cc_start: 0.7704 (tttm) cc_final: 0.7185 (ttmt)
REVERT: D   56 MET cc_start: 0.8729 (tpp) cc_final: 0.8475 (tpp)
REVERT: F   53 GLU cc_start: 0.7978 (tp30) cc_final: 0.7743 (tp30)
REVERT: F   90 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7910 (mt)
REVERT: G   73 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8462 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 133
  average time/residue: 0.1734
  time to fit residues: 30.5259
Evaluate side-chains
  141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain K residue  198 LEU
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 101 optimal weight:    0.0870
   chunk 5 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 62 optimal weight:    0.3980
   chunk 21 optimal weight:    0.5980
   chunk 108 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.211720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.123320 restraints weight = 13990.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 1.94
r_work: 0.2943 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  14237  Z= 0.134
  Angle     :  0.575   7.344  20457  Z= 0.336
  Chirality :  0.041   0.304   2313
  Planarity :  0.004   0.055   1588
  Dihedral  : 30.633 177.676   4212
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.23 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.28), residues: 913
  helix:  2.17 (0.21), residues: 583
  sheet: -0.62 (0.84), residues: 38
  loop : -0.36 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  96 
 TYR   0.010   0.001   TYR K 262 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.000   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.13 (14237)
  covalent geometry    : angle       0.57533 /  0.34 (20457)
  hydrogen bonds       : bond        0.03768 /  2.49 (  808)
  hydrogen bonds       : angle       3.01719 /  2.15 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7664 (mtm-85)
REVERT: C   56 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8221 (tm-30)
REVERT: C   95 LYS cc_start: 0.7695 (tttm) cc_final: 0.7184 (ttmt)
REVERT: D   34 TYR cc_start: 0.9257 (m-80) cc_final: 0.8877 (m-80)
REVERT: D   56 MET cc_start: 0.8721 (tpp) cc_final: 0.8467 (tpp)
REVERT: D   98 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8374 (mm)
REVERT: F   90 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7825 (mt)
REVERT: G   73 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8517 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 123
  average time/residue: 0.1693
  time to fit residues: 27.6710
Evaluate side-chains
  125 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 95 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 84 optimal weight:   30.0000
   chunk 18 optimal weight:    0.9990
   chunk 64 optimal weight:    0.3980
   chunk 8 optimal weight:    0.8980
   chunk 107 optimal weight:    8.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.219102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.130630 restraints weight = 14062.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.98
r_work: 0.2932 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14237  Z= 0.156
  Angle     :  0.584  12.660  20457  Z= 0.337
  Chirality :  0.042   0.299   2313
  Planarity :  0.004   0.035   1588
  Dihedral  : 30.619 177.220   4212
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 10.74 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.28), residues: 913
  helix:  2.15 (0.21), residues: 584
  sheet: -0.64 (0.83), residues: 38
  loop : -0.36 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  96 
 TYR   0.011   0.001   TYR G  57 
 PHE   0.009   0.001   PHE A  67 
 TRP   0.001   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.16 (14237)
  covalent geometry    : angle       0.58383 /  0.34 (20457)
  hydrogen bonds       : bond        0.03817 /  2.53 (  808)
  hydrogen bonds       : angle       3.01706 /  2.16 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7674 (mtm-85)
REVERT: C   56 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: C   95 LYS cc_start: 0.7695 (tttm) cc_final: 0.7177 (ttmt)
REVERT: D   34 TYR cc_start: 0.9270 (m-80) cc_final: 0.8904 (m-80)
REVERT: D   56 MET cc_start: 0.8730 (tpp) cc_final: 0.8466 (tpp)
REVERT: D   98 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8191 (mm)
REVERT: F   90 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7910 (mt)
REVERT: G   73 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8448 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 129
  average time/residue: 0.1741
  time to fit residues: 29.5905
Evaluate side-chains
  136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 108 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0770
   chunk 83 optimal weight:   20.0000
   chunk 74 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.219480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.131094 restraints weight = 14076.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.98
r_work: 0.2933 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2920
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14237  Z= 0.146
  Angle     :  0.580  11.658  20457  Z= 0.336
  Chirality :  0.041   0.300   2313
  Planarity :  0.004   0.047   1588
  Dihedral  : 30.610 177.176   4212
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.74 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.28), residues: 913
  helix:  2.17 (0.21), residues: 583
  sheet: -0.61 (0.83), residues: 38
  loop : -0.35 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  96 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.000   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.15 (14237)
  covalent geometry    : angle       0.57979 /  0.34 (20457)
  hydrogen bonds       : bond        0.03766 /  2.50 (  808)
  hydrogen bonds       : angle       3.00326 /  2.15 ( 2037)

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

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

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1826 Ramachandran restraints generated.
    913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7670 (mtm-85)
REVERT: C   95 LYS cc_start: 0.7691 (tttm) cc_final: 0.7176 (ttmt)
REVERT: D   34 TYR cc_start: 0.9262 (m-80) cc_final: 0.8897 (m-80)
REVERT: D   56 MET cc_start: 0.8733 (tpp) cc_final: 0.8474 (tpp)
REVERT: D   98 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8190 (mm)
REVERT: F   90 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7875 (mt)
REVERT: G   73 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8447 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 124
  average time/residue: 0.1640
  time to fit residues: 27.0759
Evaluate side-chains
  130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue  204 LYS
Chi-restraints excluded: chain K residue  214 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 103 optimal weight:   20.0000
   chunk 12 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 87 optimal weight:   20.0000
   chunk 36 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.224105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.135587 restraints weight = 14269.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.98
r_work: 0.2935 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (5 function evaluations)
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14237  Z= 0.149
  Angle     :  0.585  15.198  20457  Z= 0.336
  Chirality :  0.041   0.299   2313
  Planarity :  0.004   0.053   1588
  Dihedral  : 30.597 177.087   4212
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.87 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.28), residues: 913
  helix:  2.18 (0.21), residues: 584
  sheet: -0.58 (0.84), residues: 38
  loop : -0.33 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 129 
 TYR   0.013   0.001   TYR K 262 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.000   0.000   TRP K 349 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.15 (14237)
  covalent geometry    : angle       0.58543 /  0.34 (20457)
  hydrogen bonds       : bond        0.03759 /  2.50 (  808)
  hydrogen bonds       : angle       3.01159 /  2.15 ( 2037)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3816.52 seconds
wall clock time: 65 minutes 52.11 seconds (3952.11 seconds total)