Starting phenix.real_space_refine
on Thu Jul  2 18:06:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nzs_49958/07_2026/9nzs_49958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nzs_49958/07_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_49958/07_2026/9nzs_49958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nzs_49958/07_2026/9nzs_49958.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nzs_49958/07_2026/9nzs_49958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nzs_49958/07_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.71, per 1000 atoms: 0.18
  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: 0.84
  Conformation dependent library (CDL) restraints added in 202.8 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: 1.54

  Time building geometry restraints manager: 1.10 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: 14178
        5.79 -    11.59: 74
       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:             2.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.650
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.950
-------------------------------------------------------------------------------
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= 0.445
  Angle     :  1.274  28.965  14266  Z= 0.878
  Chirality :  0.080   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        0.00678 /  0.44 ( 9986)
  covalent geometry    : angle       1.26682 /  0.88 (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  : 0.259 
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: 0.6275 (m)
  outliers start: 3
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1043
  time to fit residues: 13.6941
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  : 0.226 
-------------------------------------------------------------------------------
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:    0.9990
   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:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3757 r_free = 0.3757 target = 0.077892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.061338 restraints weight = 49969.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.063000 restraints weight = 24025.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.063975 restraints weight = 15523.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.064395 restraints weight = 12217.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.064789 restraints weight = 10977.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.158   9990  Z= 0.339
  Angle     :  0.891  28.199  14266  Z= 0.475
  Chirality :  0.068   2.013   1669
  Planarity :  0.007   0.082   1194
  Dihedral  : 25.272 156.920   3267
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 24.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  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: -0.70 (0.30), residues: 712
  helix:  1.15 (0.26), residues: 330
  sheet: -1.96 (0.47), residues: 113
  loop : -1.80 (0.35), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.002   ARG A  38 
 TYR   0.031   0.003   TYR A  16 
 PHE   0.022   0.003   PHE B 300 
 TRP   0.023   0.003   TRP A  31 
 HIS   0.007   0.002   HIS A 217 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00717 /  0.34 ( 9986)
  covalent geometry    : angle       0.88270 /  0.47 (14260)
  hydrogen bonds       : bond        0.07697 /  5.13 (  419)
  hydrogen bonds       : angle       5.06676 /  3.49 ( 1096)
  metal coordination   : bond        0.01733 /  0.77 (    4)
  metal coordination   : angle       6.07984 /  2.76 (    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
  90 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 63
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9522 (OUTLIER) cc_final: 0.9055 (ptpt)
REVERT: A  217 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7396 (t-90)
REVERT: A  255 LYS cc_start: 0.9262 (tptp) cc_final: 0.9033 (tptp)
REVERT: A  259 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8550 (ptpp)
REVERT: A  321 CYS cc_start: 0.7083 (m) cc_final: 0.6737 (m)
REVERT: B  171 MET cc_start: 0.7450 (mmt) cc_final: 0.7241 (mmm)
REVERT: B  249 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.7124 (m-30)
REVERT: B  302 ASP cc_start: 0.9460 (t0) cc_final: 0.9257 (t70)
  outliers start: 27
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0740
  time to fit residues: 9.6428
Evaluate side-chains
  73 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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  121 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   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  246 LEU
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:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 24 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 56 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.080641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.064295 restraints weight = 48801.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.065990 restraints weight = 23142.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.066978 restraints weight = 14911.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.067617 restraints weight = 11738.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.067936 restraints weight = 10261.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9990  Z= 0.152
  Angle     :  0.733  27.811  14266  Z= 0.389
  Chirality :  0.065   2.041   1669
  Planarity :  0.005   0.066   1194
  Dihedral  : 25.160 168.194   3267
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.72 %
    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: -0.16 (0.31), residues: 712
  helix:  1.79 (0.27), residues: 329
  sheet: -1.55 (0.51), residues: 102
  loop : -1.91 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  38 
 TYR   0.016   0.002   TYR A  16 
 PHE   0.028   0.002   PHE A  23 
 TRP   0.017   0.002   TRP A  51 
 HIS   0.013   0.001   HIS A 273 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.15 ( 9986)
  covalent geometry    : angle       0.72938 /  0.39 (14260)
  hydrogen bonds       : bond        0.06095 /  4.17 (  419)
  hydrogen bonds       : angle       4.45952 /  3.04 ( 1096)
  metal coordination   : bond        0.00749 /  0.34 (    4)
  metal coordination   : angle       3.77108 /  1.93 (    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
  80 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 60
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.6804 (m-70)
REVERT: A  255 LYS cc_start: 0.9098 (tptp) cc_final: 0.8660 (tptp)
REVERT: A  259 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8299 (ptpp)
REVERT: A  321 CYS cc_start: 0.6941 (m) cc_final: 0.6589 (m)
REVERT: A  375 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.6877 (pm20)
REVERT: B  120 MET cc_start: 0.7769 (tmm) cc_final: 0.7492 (tmm)
REVERT: B  174 HIS cc_start: 0.6499 (t-90) cc_final: 0.6167 (t-90)
  outliers start: 20
  outliers final: 12
  residues processed: 79
  average time/residue: 0.0675
  time to fit residues: 7.8759
Evaluate side-chains
  73 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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 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  110 SER
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:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0000
   chunk 59 optimal weight:   20.0000
   chunk 56 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 64 optimal weight:    9.9990
   overall best weight:    2.9992

-------------------------------------------------------------------------------
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
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN
** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.077657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.060871 restraints weight = 50357.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.062483 restraints weight = 24124.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.063474 restraints weight = 15755.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.064068 restraints weight = 12377.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.064338 restraints weight = 10860.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.118   9990  Z= 0.252
  Angle     :  0.760  27.842  14266  Z= 0.405
  Chirality :  0.066   2.034   1669
  Planarity :  0.006   0.060   1194
  Dihedral  : 25.106 162.370   3267
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 19.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 24.88 %
    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: -0.16 (0.31), residues: 712
  helix:  1.64 (0.27), residues: 332
  sheet: -1.59 (0.49), residues: 112
  loop : -1.69 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  38 
 TYR   0.027   0.002   TYR A  16 
 PHE   0.015   0.002   PHE A 394 
 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        0.00528 /  0.25 ( 9986)
  covalent geometry    : angle       0.75228 /  0.41 (14260)
  hydrogen bonds       : bond        0.06550 /  4.39 (  419)
  hydrogen bonds       : angle       4.46994 /  3.08 ( 1096)
  metal coordination   : bond        0.01370 /  0.60 (    4)
  metal coordination   : angle       5.18849 /  2.37 (    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
  76 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 MET cc_start: 0.8153 (tmm) cc_final: 0.7874 (tmm)
REVERT: A  135 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9089 (ptpt)
REVERT: A  217 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7381 (m-70)
REVERT: A  255 LYS cc_start: 0.9126 (tptp) cc_final: 0.8771 (tptp)
REVERT: A  259 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8336 (ptpp)
REVERT: A  267 MET cc_start: 0.8801 (mmp) cc_final: 0.8562 (mmp)
REVERT: A  321 CYS cc_start: 0.7214 (m) cc_final: 0.6840 (m)
REVERT: B  116 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8610 (tt)
REVERT: B  120 MET cc_start: 0.7925 (tmm) cc_final: 0.7320 (tmm)
REVERT: B  128 ASN cc_start: 0.8295 (t0) cc_final: 0.7818 (t0)
REVERT: B  171 MET cc_start: 0.7605 (tpp) cc_final: 0.4763 (ttm)
REVERT: B  174 HIS cc_start: 0.7142 (t-90) cc_final: 0.6911 (t-90)
REVERT: B  196 GLN cc_start: 0.8130 (mt0) cc_final: 0.7635 (mm-40)
REVERT: B  260 MET cc_start: 0.8228 (mmm) cc_final: 0.7932 (mmp)
  outliers start: 19
  outliers final: 11
  residues processed: 75
  average time/residue: 0.0744
  time to fit residues: 8.3498
Evaluate side-chains
  71 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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  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 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  156 ASP
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  249 ASP
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:    9.9990
   chunk 53 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 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 = 0.3790 r_free = 0.3790 target = 0.079634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.063139 restraints weight = 54089.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.064790 restraints weight = 25196.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 70)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.065778 restraints weight = 16316.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.066255 restraints weight = 12934.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.066563 restraints weight = 11570.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087   9990  Z= 0.231
  Angle     :  0.738  27.877  14266  Z= 0.394
  Chirality :  0.065   2.043   1669
  Planarity :  0.006   0.101   1194
  Dihedral  : 25.111 166.180   3267
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 18.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.52 %
    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: -0.10 (0.31), residues: 712
  helix:  1.75 (0.27), residues: 330
  sheet: -1.36 (0.52), residues: 105
  loop : -1.83 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 371 
 TYR   0.038   0.002   TYR B 199 
 PHE   0.026   0.002   PHE A  23 
 TRP   0.013   0.002   TRP B  31 
 HIS   0.006   0.001   HIS A 372 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00475 /  0.23 ( 9986)
  covalent geometry    : angle       0.73196 /  0.39 (14260)
  hydrogen bonds       : bond        0.05992 /  4.07 (  419)
  hydrogen bonds       : angle       4.36506 /  3.01 ( 1096)
  metal coordination   : bond        0.01266 /  0.55 (    4)
  metal coordination   : angle       4.58382 /  2.13 (    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
  83 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 57
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8761 (t0)
REVERT: A   26 MET cc_start: 0.8028 (tmm) cc_final: 0.7674 (tmm)
REVERT: A  135 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9119 (ptpt)
REVERT: A  217 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7333 (m-70)
REVERT: A  255 LYS cc_start: 0.9117 (tptp) cc_final: 0.8695 (tptp)
REVERT: A  259 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8272 (ptpp)
REVERT: A  321 CYS cc_start: 0.7248 (m) cc_final: 0.6886 (m)
REVERT: A  375 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8050 (tp40)
REVERT: B  128 ASN cc_start: 0.8624 (t0) cc_final: 0.8358 (t0)
REVERT: B  196 GLN cc_start: 0.8145 (mt0) cc_final: 0.7745 (mm-40)
REVERT: B  260 MET cc_start: 0.8295 (mmm) cc_final: 0.8016 (mmp)
  outliers start: 26
  outliers final: 13
  residues processed: 81
  average time/residue: 0.0635
  time to fit residues: 7.6050
Evaluate side-chains
  74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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  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  273 HIS
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  156 ASP
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  189 THR
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:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 57 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    3.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 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 = 0.3769 r_free = 0.3769 target = 0.079658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.062704 restraints weight = 55549.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.064297 restraints weight = 26007.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.065257 restraints weight = 17049.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.065733 restraints weight = 13579.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.066008 restraints weight = 12187.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.108   9990  Z= 0.263
  Angle     :  0.763  27.982  14266  Z= 0.408
  Chirality :  0.066   2.044   1669
  Planarity :  0.005   0.060   1194
  Dihedral  : 25.126 164.780   3267
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 20.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.36 %
    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: -0.32 (0.31), residues: 712
  helix:  1.61 (0.27), residues: 332
  sheet: -1.73 (0.46), residues: 118
  loop : -1.89 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 379 
 TYR   0.027   0.002   TYR A  16 
 PHE   0.015   0.002   PHE A 182 
 TRP   0.013   0.002   TRP A  51 
 HIS   0.004   0.001   HIS B 361 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00542 /  0.26 ( 9986)
  covalent geometry    : angle       0.75622 /  0.41 (14260)
  hydrogen bonds       : bond        0.06277 /  4.23 (  419)
  hydrogen bonds       : angle       4.39633 /  3.03 ( 1096)
  metal coordination   : bond        0.01435 /  0.63 (    4)
  metal coordination   : angle       5.17689 /  2.36 (    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
  85 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 59
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8786 (t0)
REVERT: A   26 MET cc_start: 0.8161 (tmm) cc_final: 0.7774 (tmm)
REVERT: A  135 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9119 (ptpt)
REVERT: A  217 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7389 (m-70)
REVERT: A  255 LYS cc_start: 0.9053 (tptp) cc_final: 0.8740 (tptp)
REVERT: A  259 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8373 (ptpp)
REVERT: A  296 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9095 (tttm)
REVERT: A  321 CYS cc_start: 0.7290 (m) cc_final: 0.6945 (m)
REVERT: A  375 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8040 (tp40)
REVERT: B  174 HIS cc_start: 0.7480 (t-90) cc_final: 0.7243 (t-90)
REVERT: B  196 GLN cc_start: 0.8134 (mt0) cc_final: 0.7766 (mm-40)
  outliers start: 26
  outliers final: 16
  residues processed: 84
  average time/residue: 0.0641
  time to fit residues: 7.9191
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  : 0.164 
-------------------------------------------------------------------------------
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  100 THR
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  116 LEU
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  273 HIS
Chi-restraints excluded: chain A residue  296 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 31 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 69 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0570
   chunk 41 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   overall best weight:    3.2106

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 351 GLN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 GLN ** 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 = 0.3760 r_free = 0.3760 target = 0.079237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.062344 restraints weight = 55550.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.063910 restraints weight = 25991.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.064874 restraints weight = 17035.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.065323 restraints weight = 13538.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.065678 restraints weight = 12145.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.096   9990  Z= 0.251
  Angle     :  0.763  28.119  14266  Z= 0.404
  Chirality :  0.066   2.047   1669
  Planarity :  0.005   0.059   1194
  Dihedral  : 25.138 166.476   3267
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 25.68 %
    Favored  : 69.86 %
  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: -0.56 (0.31), residues: 712
  helix:  1.42 (0.27), residues: 338
  sheet: -1.89 (0.45), residues: 118
  loop : -2.08 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 201 
 TYR   0.026   0.002   TYR A  16 
 PHE   0.029   0.002   PHE A  23 
 TRP   0.013   0.002   TRP A  51 
 HIS   0.004   0.001   HIS A 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00514 /  0.25 ( 9986)
  covalent geometry    : angle       0.75544 /  0.40 (14260)
  hydrogen bonds       : bond        0.06169 /  4.18 (  419)
  hydrogen bonds       : angle       4.42938 /  3.05 ( 1096)
  metal coordination   : bond        0.01362 /  0.59 (    4)
  metal coordination   : angle       5.11214 /  2.37 (    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
  86 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 58
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8743 (t0)
REVERT: A   26 MET cc_start: 0.8102 (tmm) cc_final: 0.7693 (tmm)
REVERT: A  135 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9113 (ptpt)
REVERT: A  217 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7316 (m-70)
REVERT: A  255 LYS cc_start: 0.9075 (tptp) cc_final: 0.8750 (tptp)
REVERT: A  259 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8397 (ptpp)
REVERT: A  296 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9127 (tttm)
REVERT: A  321 CYS cc_start: 0.7392 (m) cc_final: 0.7043 (m)
REVERT: A  375 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8157 (tp40)
REVERT: B   14 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8529 (mm)
  outliers start: 28
  outliers final: 17
  residues processed: 84
  average time/residue: 0.0646
  time to fit residues: 8.0088
Evaluate side-chains
  80 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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   27 GLN
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  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  273 HIS
Chi-restraints excluded: chain A residue  296 LYS
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  375 GLN
Chi-restraints excluded: chain B residue   14 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0970
   chunk 11 optimal weight:    3.9990
   chunk 81 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 79 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    0.6578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
A 325 GLN
A 351 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.077937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.061555 restraints weight = 49641.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.063196 restraints weight = 23349.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.064183 restraints weight = 15073.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.064742 restraints weight = 11857.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.064993 restraints weight = 10434.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9990  Z= 0.137
  Angle     :  0.702  28.028  14266  Z= 0.367
  Chirality :  0.064   2.070   1669
  Planarity :  0.005   0.055   1194
  Dihedral  : 25.086 173.084   3267
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 27.91 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.31), residues: 712
  helix:  1.78 (0.27), residues: 336
  sheet: -1.69 (0.47), residues: 112
  loop : -2.10 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 201 
 TYR   0.026   0.002   TYR B 199 
 PHE   0.011   0.001   PHE B 212 
 TRP   0.015   0.002   TRP A  51 
 HIS   0.003   0.001   HIS B 372 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.14 ( 9986)
  covalent geometry    : angle       0.69650 /  0.37 (14260)
  hydrogen bonds       : bond        0.05521 /  3.81 (  419)
  hydrogen bonds       : angle       4.03979 /  2.75 ( 1096)
  metal coordination   : bond        0.00613 /  0.27 (    4)
  metal coordination   : angle       4.16423 /  2.07 (    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
  77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8428 (mmtm) cc_final: 0.8111 (mmmt)
REVERT: A  217 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7252 (m-70)
REVERT: A  255 LYS cc_start: 0.9054 (tptp) cc_final: 0.8696 (tptp)
REVERT: A  258 LYS cc_start: 0.9331 (tmmt) cc_final: 0.9114 (ttmm)
REVERT: A  259 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8400 (ptpp)
REVERT: A  296 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.9002 (tttm)
REVERT: A  321 CYS cc_start: 0.7041 (m) cc_final: 0.6693 (m)
REVERT: A  375 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8083 (tp40)
REVERT: B  116 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8663 (tt)
REVERT: B  249 ASP cc_start: 0.7877 (t0) cc_final: 0.7519 (m-30)
REVERT: B  260 MET cc_start: 0.8209 (mmp) cc_final: 0.7925 (mmm)
  outliers start: 18
  outliers final: 11
  residues processed: 74
  average time/residue: 0.0818
  time to fit residues: 8.8410
Evaluate side-chains
  74 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   27 GLN
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  267 MET
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  296 LYS
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  189 THR
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:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 75 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0470
   chunk 15 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.2084

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
A 325 GLN
** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3786 r_free = 0.3786 target = 0.079072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.062740 restraints weight = 53455.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.064351 restraints weight = 24826.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.065328 restraints weight = 16103.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.065790 restraints weight = 12773.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.066113 restraints weight = 11412.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   9990  Z= 0.194
  Angle     :  0.714  28.177  14266  Z= 0.374
  Chirality :  0.064   2.057   1669
  Planarity :  0.005   0.053   1194
  Dihedral  : 25.022 169.046   3267
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 17.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 27.59 %
    Favored  : 69.38 %
  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: -0.27 (0.31), residues: 712
  helix:  1.72 (0.26), residues: 338
  sheet: -1.69 (0.45), residues: 118
  loop : -2.07 (0.37), residues: 256

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   0.012   0.002   TRP A  51 
 HIS   0.004   0.001   HIS A 217 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.19 ( 9986)
  covalent geometry    : angle       0.70727 /  0.37 (14260)
  hydrogen bonds       : bond        0.05724 /  3.89 (  419)
  hydrogen bonds       : angle       4.11680 /  2.83 ( 1096)
  metal coordination   : bond        0.01020 /  0.44 (    4)
  metal coordination   : angle       4.73546 /  2.24 (    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
  79 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.9183 (ptpt)
REVERT: A  211 LYS cc_start: 0.8433 (mmtm) cc_final: 0.7977 (mmmt)
REVERT: A  217 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7311 (m-70)
REVERT: A  255 LYS cc_start: 0.9042 (tptp) cc_final: 0.8754 (tptp)
REVERT: A  259 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8389 (ptpp)
REVERT: A  260 MET cc_start: 0.8977 (mmm) cc_final: 0.8307 (tpp)
REVERT: A  296 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9043 (tttm)
REVERT: A  321 CYS cc_start: 0.7263 (m) cc_final: 0.6900 (m)
REVERT: A  375 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8137 (tp40)
REVERT: B  196 GLN cc_start: 0.8024 (mt0) cc_final: 0.7555 (mm-40)
REVERT: B  249 ASP cc_start: 0.7958 (t0) cc_final: 0.7601 (m-30)
REVERT: B  260 MET cc_start: 0.8277 (mmp) cc_final: 0.8019 (mmp)
  outliers start: 19
  outliers final: 11
  residues processed: 77
  average time/residue: 0.0879
  time to fit residues: 9.8797
Evaluate side-chains
  75 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  267 MET
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  296 LYS
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  189 THR
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:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.080704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.065097 restraints weight = 54534.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.066772 restraints weight = 26683.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.067008 restraints weight = 16092.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.067074 restraints weight = 14267.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.067215 restraints weight = 13660.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9990  Z= 0.157
  Angle     :  0.696  28.173  14266  Z= 0.362
  Chirality :  0.064   2.062   1669
  Planarity :  0.005   0.054   1194
  Dihedral  : 24.976 172.328   3267
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 27.27 %
    Favored  : 69.86 %
  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: -0.21 (0.31), residues: 712
  helix:  1.83 (0.26), residues: 336
  sheet: -1.62 (0.47), residues: 112
  loop : -2.12 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.017   0.001   TYR A  16 
 PHE   0.012   0.002   PHE A 169 
 TRP   0.012   0.001   TRP A  51 
 HIS   0.003   0.001   HIS B 361 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.16 ( 9986)
  covalent geometry    : angle       0.68950 /  0.36 (14260)
  hydrogen bonds       : bond        0.05434 /  3.73 (  419)
  hydrogen bonds       : angle       4.02536 /  2.75 ( 1096)
  metal coordination   : bond        0.00783 /  0.34 (    4)
  metal coordination   : angle       4.52364 /  2.17 (    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
  78 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.9213 (ptpt)
REVERT: A  196 GLN cc_start: 0.8308 (mp10) cc_final: 0.7991 (mp10)
REVERT: A  211 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7971 (mmmt)
REVERT: A  217 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7251 (m-70)
REVERT: A  255 LYS cc_start: 0.9135 (tptp) cc_final: 0.8782 (tptp)
REVERT: A  259 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8386 (ptpp)
REVERT: A  296 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8950 (tttm)
REVERT: A  321 CYS cc_start: 0.7176 (m) cc_final: 0.6838 (m)
REVERT: B  196 GLN cc_start: 0.8089 (mt0) cc_final: 0.7636 (mm-40)
REVERT: B  249 ASP cc_start: 0.8013 (t0) cc_final: 0.7703 (m-30)
REVERT: B  260 MET cc_start: 0.8433 (mmp) cc_final: 0.8171 (mmp)
REVERT: B  370 PRO cc_start: 0.8769 (Cg_endo) cc_final: 0.8506 (Cg_exo)
  outliers start: 18
  outliers final: 12
  residues processed: 77
  average time/residue: 0.0841
  time to fit residues: 9.4585
Evaluate side-chains
  77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  116 LEU
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  267 MET
Chi-restraints excluded: chain A residue  273 HIS
Chi-restraints excluded: chain A residue  296 LYS
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  189 THR
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:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 18 optimal weight:    0.2980
   chunk 85 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 GLN
A 375 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.080133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.063360 restraints weight = 54931.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.064969 restraints weight = 25813.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.065940 restraints weight = 16852.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.066463 restraints weight = 13348.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.066596 restraints weight = 11856.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   9990  Z= 0.183
  Angle     :  0.702  28.266  14266  Z= 0.368
  Chirality :  0.064   2.056   1669
  Planarity :  0.005   0.053   1194
  Dihedral  : 24.960 170.675   3267
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 27.43 %
    Favored  : 69.70 %
  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: -0.21 (0.31), residues: 712
  helix:  1.74 (0.26), residues: 343
  sheet: -1.63 (0.46), residues: 118
  loop : -2.09 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 376 
 TYR   0.020   0.002   TYR A  16 
 PHE   0.013   0.001   PHE A 169 
 TRP   0.012   0.002   TRP A  51 
 HIS   0.003   0.001   HIS A 217 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.18 ( 9986)
  covalent geometry    : angle       0.69491 /  0.37 (14260)
  hydrogen bonds       : bond        0.05575 /  3.79 (  419)
  hydrogen bonds       : angle       4.04080 /  2.77 ( 1096)
  metal coordination   : bond        0.00945 /  0.40 (    4)
  metal coordination   : angle       4.73867 /  2.25 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1502.64 seconds
wall clock time: 26 minutes 48.72 seconds (1608.72 seconds total)