Starting phenix.real_space_refine
on Wed Aug  5 11:18:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nzs_49958/08_2026/9nzs_49958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nzs_49958/08_2026/9nzs_49958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nzs_49958/08_2026/9nzs_49958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nzs_49958/08_2026/9nzs_49958.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nzs_49958/08_2026/9nzs_49958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nzs_49958/08_2026/9nzs_49958.map"
  }
  resolution = 3.68
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     170      5.49       5
     S      38      5.16       5
     C    5316      2.51       5
     N    1711      2.21       5
     O    2210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9446
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 412, 3295
          Classifications: {'peptide': 412}
          Link IDs: {'PTRANS': 10, 'TRANS': 401}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2548
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 9, 'TRANS': 306}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 533
          Classifications: {'DNA': 26}
          Link IDs: {'rna3p': 25}
    Chain: "D"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 163
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "E"
      Number of atoms: 2830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 2830
          Classifications: {'RNA': 132}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 9, 'rna3p_pur': 64, 'rna3p_pyr': 48}
          Link IDs: {'rna2p': 19, 'rna3p': 112}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 76
          Classifications: {'DNA': 4}
          Link IDs: {'rna3p': 3}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2922  SG  CYS A 377      16.177  83.344  73.727  1.00 53.21           S
  ATOM   2945  SG  CYS A 380      13.708  85.149  72.047  1.00 54.55           S
  ATOM   3066  SG  CYS A 396      17.476  86.297  71.919  1.00 58.95           S
  ATOM   3088  SG  CYS A 399      15.577  86.910  75.066  1.00 51.27           S

  Time building chain proxies: 2.11, per 1000 atoms: 0.22
  Number of scatterers: 9446
  At special positions: 0
  Unit cell: (93.06, 112.8, 122.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      38     16.00
     P     170     15.00
     O    2210      8.00
     N    1711      7.00
     C    5316      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: 1.18
  Conformation dependent library (CDL) restraints added in 276.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 377 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 396 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 380 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 399 "
      Number of angles added : 6


  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1364

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      51.5% alpha, 9.9% beta
      52 base pairs and 95 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 62
      removed outlier: 3.709A  pdb=" N   ARG A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU A  39 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 3.748A  pdb=" N   GLU A  71 " --> pdb=" O   ASP A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 89
      removed outlier: 3.863A  pdb=" N   HIS A  80 " --> pdb=" O   ARG A  76 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLY A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   GLN A  88 " --> pdb=" O   CYS A  84 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 111
      removed outlier: 3.585A  pdb=" N   LYS A 107 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 117
    Processing helix  chain 'A' and resid 134 through 136
      No H-bonds generated for 'chain 'A' and resid 134 through 136'
    Processing helix  chain 'A' and resid 156 through 162
      removed outlier: 3.721A  pdb=" N   GLN A 162 " --> pdb=" O   PHE A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 188
      removed outlier: 4.281A  pdb=" N   PHE A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 271
      removed outlier: 3.564A  pdb=" N   LYS A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 4.272A  pdb=" N   GLY A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 319
      removed outlier: 4.135A  pdb=" N   ASP A 295 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   LYS A 296 " --> pdb=" O   GLN A 292 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   VAL A 297 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ALA A 298 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   SER A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 361
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.612A  pdb=" N   ARG A 388 " --> pdb=" O   LYS A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 415
      removed outlier: 3.678A  pdb=" N   ILE A 415 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 427
      removed outlier: 3.929A  pdb=" N   ILE A 421 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 54
      removed outlier: 4.500A  pdb=" N   GLU B  28 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 87
      removed outlier: 4.446A  pdb=" N   GLY B  87 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 111
    Processing helix  chain 'B' and resid 111 through 117
    Processing helix  chain 'B' and resid 156 through 162
      removed outlier: 3.705A  pdb=" N   GLN B 162 " --> pdb=" O   PHE B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 188
    Processing helix  chain 'B' and resid 251 through 266
    Processing helix  chain 'B' and resid 294 through 319
    Processing helix  chain 'B' and resid 347 through 361
    Processing helix  chain 'B' and resid 407 through 415
      removed outlier: 4.163A  pdb=" N   ILE B 415 " --> pdb=" O   GLN B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 427
      removed outlier: 4.303A  pdb=" N   ASP B 419 " --> pdb=" O   ILE B 415 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS B 420 " --> pdb=" O   ARG B 416 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA B 423 " --> pdb=" O   ASP B 419 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 133
      removed outlier: 3.678A  pdb=" N   LEU A 131 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 198 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 141
      removed outlier: 3.856A  pdb=" N   ILE A 148 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 230
      removed outlier: 3.559A  pdb=" N   ASP A 228 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   GLY A 230 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ALA A 234 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 327
      removed outlier: 6.405A  pdb=" N   ILE A 324 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   ILE A 368 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   MET A 326 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 16
      removed outlier: 3.941A  pdb=" N   PHE B 205 " --> pdb=" O   TYR B 199 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   TYR B 199 " --> pdb=" O   PHE B 205 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU B 131 " --> pdb=" O   VAL B 198 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 140
      removed outlier: 4.071A  pdb=" N   PHE B 169 " --> pdb=" O   THR B 152 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 245 through 247
      removed outlier: 3.977A  pdb=" N   VAL B 227 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   GLU B 327 " --> pdb=" O   VAL B 227 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ILE B 324 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   ILE B 368 " --> pdb=" O   ILE B 324 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   MET B 326 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)

    284 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      135 hydrogen bonds
      262 hydrogen bond angles
      0 basepair planarities
      52 basepair parallelities
      95 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1645
        1.33 -     1.45: 3393
        1.45 -     1.57: 4553
        1.57 -     1.69: 337
        1.69 -     1.82: 58
  Bond restraints: 9986
  Sorted by residual:
  bond pdb=" N9   DA C  18 "
       pdb=" C4   DA C  18 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 6.00e-03 2.78e+04 2.24e+01
  bond pdb=" C3'  DA C  18 "
       pdb=" O3'  DA C  18 "
    ideal  model  delta    sigma   weight residual
    1.435  1.490 -0.055 1.30e-02 5.92e+03 1.81e+01
  bond pdb=" C3'  DC G   3 "
       pdb=" C2'  DC G   3 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.46e+01
  bond pdb=" C3'  DT C  19 "
       pdb=" O3'  DT C  19 "
    ideal  model  delta    sigma   weight residual
    1.435  1.387  0.048 1.30e-02 5.92e+03 1.36e+01
  bond pdb=" C1'  DC G   2 "
       pdb=" N1   DC G   2 "
    ideal  model  delta    sigma   weight residual
    1.468  1.517 -0.049 1.40e-02 5.10e+03 1.23e+01
  ... (remaining 9981 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.79: 14175
        5.79 -    11.59: 77
       11.59 -    17.38: 5
       17.38 -    23.17: 2
       23.17 -    28.96: 1
  Bond angle restraints: 14260
  Sorted by residual:
  angle pdb=" O3'   A E  20 "
        pdb=" P     A E  21 "
        pdb=" OP1   A E  21 "
      ideal   model   delta    sigma   weight residual
     108.00   79.04   28.96 3.00e+00 1.11e-01 9.32e+01
  angle pdb=" C1'   C E  70 "
        pdb=" N1    C E  70 "
        pdb=" C2    C E  70 "
      ideal   model   delta    sigma   weight residual
     118.80  128.03   -9.23 1.10e+00 8.26e-01 7.04e+01
  angle pdb=" CA  PRO B 214 "
        pdb=" N   PRO B 214 "
        pdb=" CD  PRO B 214 "
      ideal   model   delta    sigma   weight residual
     112.00  101.82   10.18 1.40e+00 5.10e-01 5.29e+01
  angle pdb=" N1    C E 138 "
        pdb=" C6    C E 138 "
        pdb=" C5    C E 138 "
      ideal   model   delta    sigma   weight residual
     121.00  124.62   -3.62 5.00e-01 4.00e+00 5.25e+01
  angle pdb=" O2    C E  17 "
        pdb=" C2    C E  17 "
        pdb=" N3    C E  17 "
      ideal   model   delta    sigma   weight residual
     121.90  116.95    4.95 7.00e-01 2.04e+00 5.00e+01
  ... (remaining 14255 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.71: 5349
       33.71 -    67.43: 657
       67.43 -   101.14: 68
      101.14 -   134.86: 4
      134.86 -   168.57: 5
  Dihedral angle restraints: 6083
    sinusoidal: 3965
      harmonic: 2118
  Sorted by residual:
  dihedral pdb=" O4'   C E  19 "
           pdb=" C1'   C E  19 "
           pdb=" N1    C E  19 "
           pdb=" C2    C E  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   52.44  147.56     1      1.50e+01 4.44e-03 7.87e+01
  dihedral pdb=" O4'   U E  86 "
           pdb=" C1'   U E  86 "
           pdb=" N1    U E  86 "
           pdb=" C2    U E  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   40.57 -168.57     1      1.70e+01 3.46e-03 6.58e+01
  dihedral pdb=" CA  GLY B 118 "
           pdb=" C   GLY B 118 "
           pdb=" N   SER B 119 "
           pdb=" CA  SER B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.39  -29.61     0      5.00e+00 4.00e-02 3.51e+01
  ... (remaining 6080 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.429: 1666
       0.429 -    0.858: 2
       0.858 -    1.287: 0
       1.287 -    1.716: 0
       1.716 -    2.145: 1
  Chirality restraints: 1669
  Sorted by residual:
  chirality pdb=" P     A E  21 "
            pdb=" OP1   A E  21 "
            pdb=" OP2   A E  21 "
            pdb=" O5'   A E  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.27    2.14 2.00e-01 2.50e+01 1.15e+02
  chirality pdb=" CG  LEU B 246 "
            pdb=" CB  LEU B 246 "
            pdb=" CD1 LEU B 246 "
            pdb=" CD2 LEU B 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.05   -0.54 2.00e-01 2.50e+01 7.26e+00
  chirality pdb=" CG  LEU A 185 "
            pdb=" CB  LEU A 185 "
            pdb=" CD1 LEU A 185 "
            pdb=" CD2 LEU A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.15   -0.44 2.00e-01 2.50e+01 4.86e+00
  ... (remaining 1666 not shown)

  Planarity restraints: 1194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 212 "   -0.091 5.00e-02 4.00e+02   1.33e-01 2.83e+01
        pdb=" N   PRO A 213 "    0.230 5.00e-02 4.00e+02
        pdb=" CA  PRO A 213 "   -0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO A 213 "   -0.070 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 213 "    0.078 5.00e-02 4.00e+02   1.17e-01 2.21e+01
        pdb=" N   PRO A 214 "   -0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO A 214 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO A 214 "    0.066 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G E 127 "    0.026 2.00e-02 2.50e+03   2.64e-02 2.09e+01
        pdb=" N9    G E 127 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8    G E 127 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G E 127 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    G E 127 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G E 127 "   -0.014 2.00e-02 2.50e+03
        pdb=" O6    G E 127 "    0.021 2.00e-02 2.50e+03
        pdb=" N1    G E 127 "    0.012 2.00e-02 2.50e+03
        pdb=" C2    G E 127 "   -0.069 2.00e-02 2.50e+03
        pdb=" N2    G E 127 "    0.039 2.00e-02 2.50e+03
        pdb=" N3    G E 127 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G E 127 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1191 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 3488
        2.92 -     3.41: 9291
        3.41 -     3.91: 17680
        3.91 -     4.40: 18773
        4.40 -     4.90: 27800
  Nonbonded interactions: 77032
  Sorted by model distance:
  nonbonded pdb=" N   ARG A 201 "
            pdb=" O   ARG A 201 "
     model   vdw
     2.420 2.496
  nonbonded pdb=" C3'   A E  20 "
            pdb=" OP2   A E  21 "
     model   vdw
     2.424 2.776
  nonbonded pdb=" N1    A E  34 "
            pdb=" O6    G E  64 "
     model   vdw
     2.446 2.496
  nonbonded pdb=" O5'   G E  28 "
            pdb=" O4'   G E  28 "
     model   vdw
     2.470 2.432
  nonbonded pdb=" O5'  DT C  19 "
            pdb=" O4'  DT C  19 "
     model   vdw
     2.490 2.432
  ... (remaining 77027 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.420
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
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      :  0.007   0.081   9990  Z= 0.456
  Angle     :  1.338  28.965  14266  Z= 0.945
  Chirality :  0.088   2.145   1669
  Planarity :  0.011   0.133   1194
  Dihedral  : 24.387 168.571   4719
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 27.59 %
    Favored  : 71.93 %
  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: -1.00 (0.29), residues: 712
  helix:  0.95 (0.26), residues: 326
  sheet: -2.24 (0.49), residues: 98
  loop : -1.99 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.038   0.004   ARG A  38 
 TYR   0.034   0.003   TYR A  16 
 PHE   0.032   0.005   PHE B  23 
 TRP   0.049   0.004   TRP A  31 
 HIS   0.012   0.002   HIS B 361 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00682 /  0.46 ( 9986)
  covalent geometry    : angle       1.33125 /  0.94 (14260)
  hydrogen bonds       : bond        0.14127 /  9.01 (  419)
  hydrogen bonds       : angle       5.53317 /  3.72 ( 1096)
  metal coordination   : bond        0.01162 /  0.57 (    4)
  metal coordination   : angle       6.71199 /  3.50 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 CYS cc_start: 0.6738 (m) cc_final: 0.6272 (m)
  outliers start: 3
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1166
  time to fit residues: 15.3334
Evaluate side-chains
  68 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    4.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  50 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 166 ASN
A 273 HIS
A 281 HIS
A 404 ASN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 GLN
B 129 GLN
B 305 ASN
B 412 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.078297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.061797 restraints weight = 49851.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.063378 restraints weight = 24256.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.064350 restraints weight = 15909.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.064926 restraints weight = 12608.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.065180 restraints weight = 11095.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.154   9990  Z= 0.347
  Angle     :  0.911  26.138  14266  Z= 0.479
  Chirality :  0.069   1.944   1669
  Planarity :  0.007   0.084   1194
  Dihedral  : 25.238 158.147   3267
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 23.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 23.60 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.30), residues: 712
  helix:  1.17 (0.26), residues: 330
  sheet: -1.93 (0.48), residues: 112
  loop : -1.79 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A  38 
 TYR   0.031   0.003   TYR A  16 
 PHE   0.021   0.003   PHE A 169 
 TRP   0.020   0.003   TRP B  31 
 HIS   0.007   0.001   HIS A 217 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00722 /  0.35 ( 9986)
  covalent geometry    : angle       0.90286 /  0.48 (14260)
  hydrogen bonds       : bond        0.07645 /  5.10 (  419)
  hydrogen bonds       : angle       5.05841 /  3.48 ( 1096)
  metal coordination   : bond        0.01667 /  0.74 (    4)
  metal coordination   : angle       6.07354 /  2.77 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 62
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9038 (ptpt)
REVERT: A  217 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7380 (t-90)
REVERT: A  255 LYS cc_start: 0.9221 (tptp) cc_final: 0.8971 (tptp)
REVERT: A  259 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8468 (ptpp)
REVERT: A  321 CYS cc_start: 0.7091 (m) cc_final: 0.6751 (m)
REVERT: B  249 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.7094 (m-30)
  outliers start: 27
  outliers final: 10
  residues processed: 86
  average time/residue: 0.0758
  time to fit residues: 9.8394
Evaluate side-chains
  70 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  249 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN
B 372 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.080587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.064258 restraints weight = 49010.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.065921 restraints weight = 23214.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.066898 restraints weight = 15006.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.067570 restraints weight = 11829.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.067718 restraints weight = 10270.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9990  Z= 0.153
  Angle     :  0.737  26.939  14266  Z= 0.388
  Chirality :  0.063   1.960   1669
  Planarity :  0.005   0.063   1194
  Dihedral  : 25.094 167.508   3267
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 24.72 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.31), residues: 712
  helix:  1.77 (0.26), residues: 328
  sheet: -1.54 (0.51), residues: 102
  loop : -1.93 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  38 
 TYR   0.018   0.002   TYR B 347 
 PHE   0.027   0.002   PHE A  23 
 TRP   0.016   0.002   TRP A  51 
 HIS   0.007   0.001   HIS B 361 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.15 ( 9986)
  covalent geometry    : angle       0.73310 /  0.39 (14260)
  hydrogen bonds       : bond        0.06225 /  4.24 (  419)
  hydrogen bonds       : angle       4.50639 /  3.07 ( 1096)
  metal coordination   : bond        0.00805 /  0.37 (    4)
  metal coordination   : angle       3.89771 /  1.96 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9067 (ptpt)
REVERT: A  217 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.6918 (m-70)
REVERT: A  255 LYS cc_start: 0.9101 (tptp) cc_final: 0.8718 (tptp)
REVERT: A  259 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8364 (ptpp)
REVERT: A  321 CYS cc_start: 0.6939 (m) cc_final: 0.6593 (m)
REVERT: B  120 MET cc_start: 0.7748 (tmm) cc_final: 0.7415 (tmm)
REVERT: B  174 HIS cc_start: 0.6459 (t-90) cc_final: 0.6130 (t-90)
  outliers start: 16
  outliers final: 7
  residues processed: 75
  average time/residue: 0.0908
  time to fit residues: 10.0741
Evaluate side-chains
  68 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0070
   chunk 59 optimal weight:   30.0000
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 51 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 64 optimal weight:   10.0000
   overall best weight:    1.2802

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 273 HIS
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN
B 196 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.080167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.063726 restraints weight = 49643.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.065415 restraints weight = 23512.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.066459 restraints weight = 15178.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.066982 restraints weight = 11884.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.067357 restraints weight = 10535.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9990  Z= 0.156
  Angle     :  0.706  26.678  14266  Z= 0.369
  Chirality :  0.063   1.966   1669
  Planarity :  0.005   0.055   1194
  Dihedral  : 25.014 167.741   3267
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 25.36 %
    Favored  : 72.25 %
  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: -0.01 (0.31), residues: 712
  helix:  1.91 (0.26), residues: 329
  sheet: -1.54 (0.49), residues: 112
  loop : -1.77 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  38 
 TYR   0.017   0.001   TYR A  16 
 PHE   0.014   0.002   PHE B 300 
 TRP   0.014   0.002   TRP A  51 
 HIS   0.006   0.001   HIS B 361 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.16 ( 9986)
  covalent geometry    : angle       0.70099 /  0.37 (14260)
  hydrogen bonds       : bond        0.05849 /  3.96 (  419)
  hydrogen bonds       : angle       4.30140 /  2.93 ( 1096)
  metal coordination   : bond        0.00799 /  0.36 (    4)
  metal coordination   : angle       4.09037 /  2.01 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.8077 (tmm) cc_final: 0.7835 (tmm)
REVERT: A  135 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9095 (ptpt)
REVERT: A  217 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7372 (m-70)
REVERT: A  255 LYS cc_start: 0.9086 (tptp) cc_final: 0.8690 (tptp)
REVERT: A  259 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8289 (ptpp)
REVERT: A  321 CYS cc_start: 0.6980 (m) cc_final: 0.6649 (m)
REVERT: B  116 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8606 (tt)
REVERT: B  120 MET cc_start: 0.7797 (tmm) cc_final: 0.7285 (tmm)
REVERT: B  174 HIS cc_start: 0.6748 (t-90) cc_final: 0.6415 (t-90)
REVERT: B  196 GLN cc_start: 0.7979 (mt0) cc_final: 0.7657 (mm-40)
REVERT: B  260 MET cc_start: 0.8193 (mmm) cc_final: 0.7936 (mmm)
  outliers start: 15
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0833
  time to fit residues: 8.7855
Evaluate side-chains
  72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0980
   chunk 45 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 67 optimal weight:   20.0000
   chunk 24 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 37 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0050
   overall best weight:    3.3598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
** A  98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.077757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.061072 restraints weight = 50235.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.062671 restraints weight = 24062.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.063657 restraints weight = 15750.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.064197 restraints weight = 12388.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.064197 restraints weight = 10943.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.111   9990  Z= 0.255
  Angle     :  0.774  26.685  14266  Z= 0.405
  Chirality :  0.065   1.952   1669
  Planarity :  0.006   0.096   1194
  Dihedral  : 25.036 163.713   3267
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 19.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.24 %
    Favored  : 72.25 %
  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: -0.11 (0.31), residues: 712
  helix:  1.79 (0.26), residues: 330
  sheet: -1.41 (0.50), residues: 108
  loop : -1.89 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  38 
 TYR   0.026   0.002   TYR A  16 
 PHE   0.022   0.002   PHE A  23 
 TRP   0.012   0.002   TRP B  31 
 HIS   0.009   0.001   HIS A 273 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00524 /  0.26 ( 9986)
  covalent geometry    : angle       0.76706 /  0.40 (14260)
  hydrogen bonds       : bond        0.06352 /  4.27 (  419)
  hydrogen bonds       : angle       4.41257 /  3.04 ( 1096)
  metal coordination   : bond        0.01371 /  0.60 (    4)
  metal coordination   : angle       5.00291 /  2.29 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.8118 (tmm) cc_final: 0.7833 (tmm)
REVERT: A  135 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9085 (ptpt)
REVERT: A  217 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.7381 (m-70)
REVERT: A  255 LYS cc_start: 0.9107 (tptp) cc_final: 0.8654 (tptp)
REVERT: A  259 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8403 (ptpp)
REVERT: A  321 CYS cc_start: 0.7246 (m) cc_final: 0.6869 (m)
REVERT: A  375 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7913 (tp40)
REVERT: B  116 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8633 (tt)
REVERT: B  196 GLN cc_start: 0.8040 (mt0) cc_final: 0.7673 (mm-40)
REVERT: B  260 MET cc_start: 0.8200 (mmm) cc_final: 0.7919 (mmp)
  outliers start: 22
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0833
  time to fit residues: 9.8446
Evaluate side-chains
  72 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 62 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 81 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    3.2786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
A 273 HIS
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.076640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.059976 restraints weight = 50564.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.061579 restraints weight = 24081.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.062562 restraints weight = 15633.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.063028 restraints weight = 12303.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.063332 restraints weight = 10977.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107   9990  Z= 0.247
  Angle     :  0.782  26.967  14266  Z= 0.407
  Chirality :  0.065   1.970   1669
  Planarity :  0.006   0.060   1194
  Dihedral  : 25.100 165.862   3267
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 19.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 24.88 %
    Favored  : 70.49 %
  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: -0.37 (0.31), residues: 712
  helix:  1.59 (0.27), residues: 336
  sheet: -1.58 (0.51), residues: 102
  loop : -2.10 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 263 
 TYR   0.027   0.002   TYR A  16 
 PHE   0.013   0.002   PHE B 212 
 TRP   0.012   0.002   TRP B  31 
 HIS   0.005   0.001   HIS B 361 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00510 /  0.25 ( 9986)
  covalent geometry    : angle       0.77556 /  0.41 (14260)
  hydrogen bonds       : bond        0.06107 /  4.12 (  419)
  hydrogen bonds       : angle       4.38511 /  3.02 ( 1096)
  metal coordination   : bond        0.01430 /  0.63 (    4)
  metal coordination   : angle       4.80529 /  2.21 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 61
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8730 (t0)
REVERT: A   26 MET cc_start: 0.8135 (tmm) cc_final: 0.7739 (tmm)
REVERT: A  135 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9131 (ptpt)
REVERT: A  171 MET cc_start: 0.8274 (mtm) cc_final: 0.8041 (mtt)
REVERT: A  217 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7327 (m-70)
REVERT: A  255 LYS cc_start: 0.9134 (tptp) cc_final: 0.8827 (tptp)
REVERT: A  259 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8264 (ptpp)
REVERT: A  260 MET cc_start: 0.8636 (tpp) cc_final: 0.8248 (tpp)
REVERT: A  321 CYS cc_start: 0.7337 (m) cc_final: 0.6966 (m)
REVERT: B  116 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8608 (tt)
REVERT: B  174 HIS cc_start: 0.7369 (t-90) cc_final: 0.7141 (t-90)
REVERT: B  196 GLN cc_start: 0.7981 (mt0) cc_final: 0.7655 (mm-40)
REVERT: B  260 MET cc_start: 0.8253 (mmm) cc_final: 0.8042 (mmm)
  outliers start: 29
  outliers final: 19
  residues processed: 87
  average time/residue: 0.0899
  time to fit residues: 11.6052
Evaluate side-chains
  82 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   25 ASN
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain B residue   16 TYR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 78 optimal weight:   30.0000
   chunk 31 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0970
   chunk 5 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 86 optimal weight:   20.0000
   chunk 56 optimal weight:    9.9990
   overall best weight:    3.4186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
A 273 HIS
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.076063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.059443 restraints weight = 51042.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.061002 restraints weight = 24529.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.061935 restraints weight = 16085.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.062407 restraints weight = 12749.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.062712 restraints weight = 11374.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.102   9990  Z= 0.261
  Angle     :  0.785  27.072  14266  Z= 0.407
  Chirality :  0.066   1.979   1669
  Planarity :  0.005   0.059   1194
  Dihedral  : 25.068 165.435   3267
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 20.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 25.36 %
    Favored  : 70.18 %
  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: -0.54 (0.31), residues: 712
  helix:  1.47 (0.26), residues: 338
  sheet: -1.99 (0.45), residues: 118
  loop : -2.05 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 263 
 TYR   0.024   0.002   TYR A  16 
 PHE   0.027   0.002   PHE A  23 
 TRP   0.013   0.002   TRP B  31 
 HIS   0.012   0.001   HIS A 273 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00541 /  0.26 ( 9986)
  covalent geometry    : angle       0.77792 /  0.41 (14260)
  hydrogen bonds       : bond        0.06292 /  4.24 (  419)
  hydrogen bonds       : angle       4.36705 /  3.01 ( 1096)
  metal coordination   : bond        0.01496 /  0.65 (    4)
  metal coordination   : angle       5.19712 /  2.38 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8734 (t0)
REVERT: A   26 MET cc_start: 0.8127 (tmm) cc_final: 0.7704 (tmm)
REVERT: A  135 LYS cc_start: 0.9504 (OUTLIER) cc_final: 0.9134 (ptpt)
REVERT: A  171 MET cc_start: 0.8243 (mtm) cc_final: 0.8010 (mtt)
REVERT: A  217 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7330 (m-70)
REVERT: A  255 LYS cc_start: 0.9066 (tptp) cc_final: 0.8807 (tptp)
REVERT: A  259 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8384 (ptpp)
REVERT: A  260 MET cc_start: 0.8663 (tpp) cc_final: 0.8426 (tpp)
REVERT: A  296 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9072 (tttm)
REVERT: A  321 CYS cc_start: 0.7316 (m) cc_final: 0.6964 (m)
REVERT: B  171 MET cc_start: 0.7206 (mmp) cc_final: 0.5107 (ttm)
REVERT: B  196 GLN cc_start: 0.7969 (mt0) cc_final: 0.7663 (mm-40)
REVERT: B  260 MET cc_start: 0.8298 (mmm) cc_final: 0.8075 (mmm)
  outliers start: 28
  outliers final: 17
  residues processed: 79
  average time/residue: 0.0817
  time to fit residues: 9.5465
Evaluate side-chains
  77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 55
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   25 ASN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  186 MET
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  249 ASP
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 81 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.077863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.060745 restraints weight = 51625.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.062330 restraints weight = 24799.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.063266 restraints weight = 16271.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.063858 restraints weight = 12921.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.064138 restraints weight = 11381.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9990  Z= 0.184
  Angle     :  0.735  27.235  14266  Z= 0.379
  Chirality :  0.064   2.001   1669
  Planarity :  0.005   0.058   1194
  Dihedral  : 25.028 169.622   3267
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 17.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 26.16 %
    Favored  : 70.49 %
  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: -0.45 (0.31), residues: 712
  helix:  1.66 (0.26), residues: 338
  sheet: -2.06 (0.47), residues: 106
  loop : -2.16 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 263 
 TYR   0.021   0.002   TYR A  16 
 PHE   0.015   0.002   PHE A 169 
 TRP   0.013   0.002   TRP A  51 
 HIS   0.004   0.001   HIS B 372 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.18 ( 9986)
  covalent geometry    : angle       0.72918 /  0.38 (14260)
  hydrogen bonds       : bond        0.05782 /  3.93 (  419)
  hydrogen bonds       : angle       4.09669 /  2.82 ( 1096)
  metal coordination   : bond        0.01013 /  0.44 (    4)
  metal coordination   : angle       4.42804 /  2.12 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9189 (ptpt)
REVERT: A  196 GLN cc_start: 0.8217 (mp10) cc_final: 0.7926 (mp10)
REVERT: A  217 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7327 (m-70)
REVERT: A  255 LYS cc_start: 0.9095 (tptp) cc_final: 0.8811 (tptp)
REVERT: A  259 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8429 (ptpp)
REVERT: A  260 MET cc_start: 0.8705 (tpp) cc_final: 0.8412 (tpp)
REVERT: A  296 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8921 (tttm)
REVERT: A  321 CYS cc_start: 0.7198 (m) cc_final: 0.6853 (m)
REVERT: B  116 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8690 (tt)
REVERT: B  171 MET cc_start: 0.7272 (mmp) cc_final: 0.5468 (mtt)
REVERT: B  196 GLN cc_start: 0.7978 (mt0) cc_final: 0.7679 (mm-40)
REVERT: B  260 MET cc_start: 0.8392 (mmm) cc_final: 0.8132 (mmm)
  outliers start: 21
  outliers final: 15
  residues processed: 75
  average time/residue: 0.0805
  time to fit residues: 8.8545
Evaluate side-chains
  77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 268 GLN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.078340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.062119 restraints weight = 49627.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.063721 restraints weight = 23738.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.064672 restraints weight = 15425.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.065255 restraints weight = 12184.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.065451 restraints weight = 10690.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9990  Z= 0.142
  Angle     :  0.731  27.189  14266  Z= 0.368
  Chirality :  0.063   2.016   1669
  Planarity :  0.005   0.055   1194
  Dihedral  : 24.955 172.966   3267
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 27.11 %
    Favored  : 70.33 %
  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: -0.25 (0.32), residues: 712
  helix:  1.86 (0.27), residues: 336
  sheet: -1.90 (0.46), residues: 113
  loop : -2.10 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 263 
 TYR   0.015   0.001   TYR A  16 
 PHE   0.028   0.002   PHE A  23 
 TRP   0.014   0.002   TRP A  51 
 HIS   0.003   0.001   HIS B 361 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.14 ( 9986)
  covalent geometry    : angle       0.72571 /  0.37 (14260)
  hydrogen bonds       : bond        0.05430 /  3.71 (  419)
  hydrogen bonds       : angle       3.88199 /  2.64 ( 1096)
  metal coordination   : bond        0.00642 /  0.28 (    4)
  metal coordination   : angle       4.27190 /  2.13 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLN cc_start: 0.8158 (mp10) cc_final: 0.7868 (mp10)
REVERT: A  217 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.7296 (m-70)
REVERT: A  255 LYS cc_start: 0.9045 (tptp) cc_final: 0.8694 (tptp)
REVERT: A  259 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8374 (ptpp)
REVERT: A  260 MET cc_start: 0.8631 (tpp) cc_final: 0.8317 (tpp)
REVERT: A  321 CYS cc_start: 0.7027 (m) cc_final: 0.6673 (m)
REVERT: B  171 MET cc_start: 0.7228 (mmp) cc_final: 0.5500 (mtt)
REVERT: B  196 GLN cc_start: 0.7927 (mt0) cc_final: 0.7684 (mm-40)
REVERT: B  249 ASP cc_start: 0.7855 (t0) cc_final: 0.7542 (m-30)
REVERT: B  260 MET cc_start: 0.8336 (mmm) cc_final: 0.8092 (mmm)
  outliers start: 16
  outliers final: 13
  residues processed: 74
  average time/residue: 0.0882
  time to fit residues: 9.5123
Evaluate side-chains
  74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 66 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 85 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 74 optimal weight:   10.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  29 GLN
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.078627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.062399 restraints weight = 49601.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.063988 restraints weight = 23726.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.064951 restraints weight = 15444.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.065447 restraints weight = 12238.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.065770 restraints weight = 10856.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9990  Z= 0.135
  Angle     :  0.706  27.219  14266  Z= 0.357
  Chirality :  0.063   2.018   1669
  Planarity :  0.004   0.053   1194
  Dihedral  : 24.899 173.557   3267
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 27.43 %
    Favored  : 70.18 %
  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: -0.22 (0.31), residues: 712
  helix:  1.85 (0.27), residues: 338
  sheet: -1.90 (0.51), residues: 94
  loop : -2.11 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 263 
 TYR   0.016   0.001   TYR A  16 
 PHE   0.016   0.002   PHE A 169 
 TRP   0.012   0.002   TRP A  51 
 HIS   0.003   0.001   HIS B 361 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.13 ( 9986)
  covalent geometry    : angle       0.70121 /  0.36 (14260)
  hydrogen bonds       : bond        0.05346 /  3.64 (  419)
  hydrogen bonds       : angle       3.80409 /  2.59 ( 1096)
  metal coordination   : bond        0.00599 /  0.26 (    4)
  metal coordination   : angle       4.21100 /  2.08 (    6)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 GLN cc_start: 0.8175 (mp10) cc_final: 0.7885 (mp10)
REVERT: A  217 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.7275 (m-70)
REVERT: A  255 LYS cc_start: 0.9003 (tptp) cc_final: 0.8561 (tptp)
REVERT: A  258 LYS cc_start: 0.9296 (tmmt) cc_final: 0.9066 (ttmm)
REVERT: A  259 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8315 (ptpp)
REVERT: A  260 MET cc_start: 0.8606 (tpp) cc_final: 0.8321 (tpp)
REVERT: A  321 CYS cc_start: 0.7024 (m) cc_final: 0.6670 (m)
REVERT: B  171 MET cc_start: 0.7297 (mmp) cc_final: 0.5582 (mtt)
REVERT: B  249 ASP cc_start: 0.7889 (t0) cc_final: 0.7585 (m-30)
REVERT: B  260 MET cc_start: 0.8343 (mmm) cc_final: 0.8143 (mmm)
  outliers start: 15
  outliers final: 12
  residues processed: 75
  average time/residue: 0.0859
  time to fit residues: 9.6239
Evaluate side-chains
  75 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  135 LYS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  210 TYR
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  259 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   80 HIS
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain B residue  324 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 80 optimal weight:   20.0000
   chunk 76 optimal weight:   20.0000
   chunk 18 optimal weight:    4.9990
   chunk 85 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 83 optimal weight:   20.0000
   chunk 15 optimal weight:    0.0470
   chunk 30 optimal weight:    0.9990
   overall best weight:    3.2086

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.075353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.058197 restraints weight = 50096.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.059786 restraints weight = 24039.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.060709 restraints weight = 15764.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.061286 restraints weight = 12518.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.061542 restraints weight = 11040.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.4143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.109   9990  Z= 0.244
  Angle     :  0.788  27.306  14266  Z= 0.400
  Chirality :  0.065   2.005   1669
  Planarity :  0.005   0.054   1194
  Dihedral  : 24.915 167.620   3267
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 27.11 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.51 (0.31), residues: 712
  helix:  1.54 (0.26), residues: 344
  sheet: -1.98 (0.45), residues: 118
  loop : -2.19 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 263 
 TYR   0.027   0.002   TYR A  16 
 PHE   0.028   0.002   PHE A  23 
 TRP   0.011   0.002   TRP B  51 
 HIS   0.005   0.001   HIS A 217 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00509 /  0.24 ( 9986)
  covalent geometry    : angle       0.78115 /  0.40 (14260)
  hydrogen bonds       : bond        0.06171 /  4.14 (  419)
  hydrogen bonds       : angle       4.13508 /  2.85 ( 1096)
  metal coordination   : bond        0.01383 /  0.61 (    4)
  metal coordination   : angle       5.25793 /  2.47 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1663.83 seconds
wall clock time: 29 minutes 37.53 seconds (1777.53 seconds total)