Starting phenix.real_space_refine
on Tue Feb  3 22:46:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n9c_49165/02_2026/9n9c_49165.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n9c_49165/02_2026/9n9c_49165.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n9c_49165/02_2026/9n9c_49165.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n9c_49165/02_2026/9n9c_49165.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n9c_49165/02_2026/9n9c_49165.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n9c_49165/02_2026/9n9c_49165.cif"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      88      5.49       5
     Mg      1      5.21       5
     S      30      5.16       5
     C    4520      2.51       5
     N    1353      2.21       5
     O    1610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7602
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2860
          Classifications: {'peptide': 346}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 338}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2860
          Classifications: {'peptide': 346}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 338}
          Chain breaks: 1
    Chain: "c"
      Number of atoms: 1881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 1881
          Classifications: {'RNA': 88}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 44, 'rna3p_pyr': 35}
          Link IDs: {'rna2p': 9, 'rna3p': 78}
    Chain: "c"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.82, per 1000 atoms: 0.24
  Number of scatterers: 7602
  At special positions: 0
  Unit cell: (84.666, 107.682, 100.284, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      30     16.00
     P      88     15.00
     Mg      1     11.99
     O    1610      8.00
     N    1353      7.00
     C    4520      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: 0.54
  Conformation dependent library (CDL) restraints added in 202.6 milliseconds
  

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1308

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 6 sheets defined
      48.0% alpha, 25.0% beta
      25 base pairs and 44 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 63
      removed outlier: 3.835A  pdb=" N   LYS A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 96
    Processing helix  chain 'A' and resid 102 through 119
    Processing helix  chain 'A' and resid 119 through 126
    Processing helix  chain 'A' and resid 177 through 188
      removed outlier: 3.677A  pdb=" N   LYS A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 270
      removed outlier: 4.308A  pdb=" N   TYR A 254 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   ARG A 255 " --> pdb=" O   GLU A 251 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 4.246A  pdb=" N   ARG A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 315
      removed outlier: 4.236A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS A 290 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 359
      removed outlier: 3.900A  pdb=" N   TYR A 353 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ALA A 358 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 54
    Processing helix  chain 'B' and resid 84 through 96
      removed outlier: 4.207A  pdb=" N   THR B  88 " --> pdb=" O   ARG B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 126
      removed outlier: 3.612A  pdb=" N   LEU B 105 " --> pdb=" O   PRO B 101 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   VAL B 121 " --> pdb=" O   ASN B 117 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   GLN B 122 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 188
    Processing helix  chain 'B' and resid 248 through 272
      removed outlier: 4.713A  pdb=" N   ARG B 255 " --> pdb=" O   GLU B 251 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ARG B 256 " --> pdb=" O   PHE B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 315
      removed outlier: 5.396A  pdb=" N   ALA B 285 " --> pdb=" O   ARG B 281 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   VAL B 286 " --> pdb=" O   LYS B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 359
    Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141
      removed outlier: 4.137A  pdb=" N   ILE A 204 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   PHE A 158 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ALA A 157 " --> pdb=" O   TYR A 151 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   TYR A 151 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   CYS A 159 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU A 149 " --> pdb=" O   CYS A 159 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 141
      removed outlier: 4.636A  pdb=" N   LYS A 191 " --> pdb=" O   GLU A 211 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 246
      removed outlier: 3.604A  pdb=" N   ILE A 235 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   ALA A 317 " --> pdb=" O   PRO A 221 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   VAL A 223 " --> pdb=" O   ALA A 317 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   THR A 319 " --> pdb=" O   VAL A 223 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 225 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE A 321 " --> pdb=" O   ALA A 225 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   MET A 323 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 141
      removed outlier: 3.732A  pdb=" N   SER B 195 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   ILE B 204 " --> pdb=" O   ILE B  14 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   PHE B 158 " --> pdb=" O   THR B 169 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA B 157 " --> pdb=" O   TYR B 151 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   TYR B 151 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   CYS B 159 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   LEU B 149 " --> pdb=" O   CYS B 159 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 141
      removed outlier: 3.732A  pdb=" N   SER B 195 " --> pdb=" O   PHE B 141 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 242 through 246
      removed outlier: 3.755A  pdb=" N   ILE B 235 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 8.429A  pdb=" N   ALA B 317 " --> pdb=" O   PRO B 221 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   VAL B 223 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   GLY B 318 " --> pdb=" O   GLU B 361 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   ILE B 363 " --> pdb=" O   GLY B 318 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   LEU B 320 " --> pdb=" O   ILE B 363 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   GLY B 365 " --> pdb=" O   LEU B 320 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU B 322 " --> pdb=" O   GLY B 365 " (cutoff:3.500A)

    353 hydrogen bonds defined for protein.
    1014 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      62 hydrogen bonds
      112 hydrogen bond angles
      0 basepair planarities
      25 basepair parallelities
      44 stacking parallelities
  Total time for adding SS restraints: 1.14

  Time building geometry restraints manager: 0.74 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: 1801
        1.33 -     1.45: 2023
        1.45 -     1.57: 3884
        1.57 -     1.69: 175
        1.69 -     1.81: 52
  Bond restraints: 7935
  Sorted by residual:
  bond pdb=" CG1 ILE B 246 "
       pdb=" CD1 ILE B 246 "
    ideal  model  delta    sigma   weight residual
    1.513  1.456  0.057 3.90e-02 6.57e+02 2.14e+00
  bond pdb=" CG  ARG A 281 "
       pdb=" CD  ARG A 281 "
    ideal  model  delta    sigma   weight residual
    1.520  1.479  0.041 3.00e-02 1.11e+03 1.89e+00
  bond pdb=" CA  TYR B 345 "
       pdb=" C   TYR B 345 "
    ideal  model  delta    sigma   weight residual
    1.523  1.506  0.017 1.34e-02 5.57e+03 1.58e+00
  bond pdb=" CB  TYR A 296 "
       pdb=" CG  TYR A 296 "
    ideal  model  delta    sigma   weight residual
    1.512  1.485  0.027 2.20e-02 2.07e+03 1.45e+00
  bond pdb=" CG  LEU B 322 "
       pdb=" CD1 LEU B 322 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.21e+00
  ... (remaining 7930 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 11000
        2.68 -     5.36: 71
        5.36 -     8.03: 8
        8.03 -    10.71: 1
       10.71 -    13.39: 1
  Bond angle restraints: 11081
  Sorted by residual:
  angle pdb=" CG  ARG B 184 "
        pdb=" CD  ARG B 184 "
        pdb=" NE  ARG B 184 "
      ideal   model   delta    sigma   weight residual
     112.00  119.69   -7.69 2.20e+00 2.07e-01 1.22e+01
  angle pdb=" C2'   G c  28 "
        pdb=" C1'   G c  28 "
        pdb=" N9    G c  28 "
      ideal   model   delta    sigma   weight residual
     114.00  109.16    4.84 1.50e+00 4.44e-01 1.04e+01
  angle pdb=" CB  ARG A 164 "
        pdb=" CG  ARG A 164 "
        pdb=" CD  ARG A 164 "
      ideal   model   delta    sigma   weight residual
     111.30  118.10   -6.80 2.30e+00 1.89e-01 8.73e+00
  angle pdb=" C   ASN B 324 "
        pdb=" N   GLN B 325 "
        pdb=" CA  GLN B 325 "
      ideal   model   delta    sigma   weight residual
     121.54  126.91   -5.37 1.91e+00 2.74e-01 7.91e+00
  angle pdb=" O4'   G c  28 "
        pdb=" C1'   G c  28 "
        pdb=" N9    G c  28 "
      ideal   model   delta    sigma   weight residual
     108.20  112.32   -4.12 1.50e+00 4.44e-01 7.55e+00
  ... (remaining 11076 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.72: 4507
       32.72 -    65.45: 362
       65.45 -    98.17: 28
       98.17 -   130.89: 0
      130.89 -   163.62: 1
  Dihedral angle restraints: 4898
    sinusoidal: 2869
      harmonic: 2029
  Sorted by residual:
  dihedral pdb=" O4'   C c  13 "
           pdb=" C1'   C c  13 "
           pdb=" N1    C c  13 "
           pdb=" C2    C c  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   36.38  163.62     1      1.50e+01 4.44e-03 8.36e+01
  dihedral pdb=" CA  MET B  85 "
           pdb=" C   MET B  85 "
           pdb=" N   ASN B  86 "
           pdb=" CA  ASN B  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.83  -20.17     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  TYR A 272 "
           pdb=" C   TYR A 272 "
           pdb=" N   SER A 273 "
           pdb=" CA  SER A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.51   16.49     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 4895 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 808
       0.032 -    0.063: 343
       0.063 -    0.095: 78
       0.095 -    0.127: 45
       0.127 -    0.158: 10
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" CB  THR B 292 "
            pdb=" CA  THR B 292 "
            pdb=" OG1 THR B 292 "
            pdb=" CG2 THR B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CB  ILE B  14 "
            pdb=" CA  ILE B  14 "
            pdb=" CG1 ILE B  14 "
            pdb=" CG2 ILE B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CA  ILE B 246 "
            pdb=" N   ILE B 246 "
            pdb=" C   ILE B 246 "
            pdb=" CB  ILE B 246 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 1281 not shown)

  Planarity restraints: 1057
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G c  28 "   -0.061 2.00e-02 2.50e+03   2.64e-02 2.09e+01
        pdb=" N9    G c  28 "    0.064 2.00e-02 2.50e+03
        pdb=" C8    G c  28 "    0.008 2.00e-02 2.50e+03
        pdb=" N7    G c  28 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    G c  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G c  28 "   -0.014 2.00e-02 2.50e+03
        pdb=" O6    G c  28 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    G c  28 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    G c  28 "    0.003 2.00e-02 2.50e+03
        pdb=" N2    G c  28 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    G c  28 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    G c  28 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 184 "    0.255 9.50e-02 1.11e+02   1.15e-01 8.37e+00
        pdb=" NE  ARG B 184 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 184 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 184 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 184 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A c  53 "   -0.024 2.00e-02 2.50e+03   1.20e-02 3.95e+00
        pdb=" N9    A c  53 "    0.031 2.00e-02 2.50e+03
        pdb=" C8    A c  53 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A c  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A c  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A c  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A c  53 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A c  53 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A c  53 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A c  53 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    A c  53 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1054 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 109
        2.64 -     3.20: 6572
        3.20 -     3.77: 12627
        3.77 -     4.33: 16647
        4.33 -     4.90: 25229
  Nonbonded interactions: 61184
  Sorted by model distance:
  nonbonded pdb=" N2    G c  16 "
            pdb=" O2    C c  71 "
     model   vdw
     2.073 2.496
  nonbonded pdb=" NH1 ARG A  10 "
            pdb=" OP2   U c  75 "
     model   vdw
     2.136 3.120
  nonbonded pdb=" O   GLU A 251 "
            pdb=" OH  TYR A 296 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" ND2 ASN A  43 "
            pdb=" O   GLU B 127 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" O2'   C c  23 "
            pdb=" N3    A c  53 "
     model   vdw
     2.248 3.120
  ... (remaining 61179 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.410
  Find NCS groups from input model:        0.080
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
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      :  0.005   0.057   7935  Z= 0.221
  Angle     :  0.625  13.388  11081  Z= 0.330
  Chirality :  0.040   0.158   1284
  Planarity :  0.005   0.115   1057
  Dihedral  : 19.867 163.616   3590
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.43 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 27.51 %
    Favored  : 68.61 %
  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: -0.44 (0.32), residues: 682
  helix:  1.29 (0.29), residues: 319
  sheet: -0.66 (0.50), residues: 113
  loop : -2.25 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 184 
 TYR   0.012   0.001   TYR B 254 
 PHE   0.021   0.002   PHE A  39 
 TRP   0.026   0.002   TRP B 342 
 HIS   0.005   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 7935)
  covalent geometry    : angle       0.62464 (11081)
  hydrogen bonds       : bond        0.13996 (  396)
  hydrogen bonds       : angle       5.71326 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASP cc_start: 0.7458 (m-30) cc_final: 0.7162 (m-30)
REVERT: A   53 GLU cc_start: 0.7394 (tt0) cc_final: 0.5945 (tt0)
REVERT: A  130 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6565 (mp)
REVERT: A  134 LYS cc_start: 0.7435 (mmtt) cc_final: 0.7193 (mmtt)
REVERT: A  174 ASP cc_start: 0.7733 (t0) cc_final: 0.7271 (t0)
REVERT: A  184 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7229 (mtp85)
REVERT: A  263 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7542 (ttm170)
REVERT: B   57 ASP cc_start: 0.6885 (m-30) cc_final: 0.6617 (m-30)
REVERT: B   91 VAL cc_start: 0.7885 (t) cc_final: 0.7640 (p)
REVERT: B  100 MET cc_start: 0.4754 (tpt) cc_final: 0.3979 (tpt)
REVERT: B  139 PHE cc_start: 0.7723 (p90) cc_final: 0.7273 (p90)
REVERT: B  223 VAL cc_start: 0.8678 (p) cc_final: 0.8352 (m)
REVERT: B  231 LEU cc_start: 0.8798 (mt) cc_final: 0.8591 (mt)
REVERT: B  232 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6954 (mm-30)
REVERT: B  241 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7703 (tmtt)
REVERT: B  342 TRP cc_start: 0.8414 (m100) cc_final: 0.8154 (m100)
  outliers start: 24
  outliers final: 21
  residues processed: 148
  average time/residue: 0.1161
  time to fit residues: 21.3277
Evaluate side-chains
  158 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  293 GLU
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   85 MET
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  164 ARG
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 315 HIS
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** 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 = 0.4267 r_free = 0.4267 target = 0.185193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.152762 restraints weight = 11041.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.30
r_work: 0.3753 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.0865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7935  Z= 0.155
  Angle     :  0.532  11.567  11081  Z= 0.279
  Chirality :  0.037   0.164   1284
  Planarity :  0.004   0.038   1057
  Dihedral  : 19.007 161.563   2157
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.84 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 24.27 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.32), residues: 682
  helix:  1.73 (0.28), residues: 318
  sheet: -0.72 (0.48), residues: 124
  loop : -2.04 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 300 
 TYR   0.010   0.001   TYR B 353 
 PHE   0.016   0.002   PHE A  39 
 TRP   0.009   0.001   TRP B 342 
 HIS   0.005   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7935)
  covalent geometry    : angle       0.53154 (11081)
  hydrogen bonds       : bond        0.05144 (  396)
  hydrogen bonds       : angle       4.35220 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 132
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7346 (tt0) cc_final: 0.5873 (tt0)
REVERT: A  134 LYS cc_start: 0.7433 (mmtt) cc_final: 0.7178 (mmtt)
REVERT: A  184 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7408 (mtm-85)
REVERT: A  214 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8163 (ptpt)
REVERT: A  263 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7537 (ttm170)
REVERT: A  280 LYS cc_start: 0.7955 (mttt) cc_final: 0.7635 (mttp)
REVERT: B   57 ASP cc_start: 0.6895 (m-30) cc_final: 0.6607 (m-30)
REVERT: B   91 VAL cc_start: 0.7888 (t) cc_final: 0.7654 (p)
REVERT: B  113 ILE cc_start: 0.7671 (mt) cc_final: 0.7460 (mt)
REVERT: B  139 PHE cc_start: 0.7748 (p90) cc_final: 0.7296 (p90)
REVERT: B  146 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5743 (tt)
REVERT: B  191 LYS cc_start: 0.7090 (tttt) cc_final: 0.6839 (tttm)
REVERT: B  232 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6894 (mm-30)
REVERT: B  241 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7649 (tmtt)
REVERT: B  246 ILE cc_start: 0.7449 (mm) cc_final: 0.7231 (mt)
REVERT: B  342 TRP cc_start: 0.8499 (m100) cc_final: 0.8283 (m100)
  outliers start: 36
  outliers final: 20
  residues processed: 153
  average time/residue: 0.1368
  time to fit residues: 26.0045
Evaluate side-chains
  148 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  125 LYS
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  128 ARG
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** 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 = 0.4245 r_free = 0.4245 target = 0.183416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.150461 restraints weight = 10966.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 2.37
r_work: 0.3720 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.1064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7935  Z= 0.228
  Angle     :  0.576  11.640  11081  Z= 0.300
  Chirality :  0.040   0.193   1284
  Planarity :  0.004   0.047   1057
  Dihedral  : 18.883 163.709   2128
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.28 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  7.28 %
    Allowed  : 23.30 %
    Favored  : 69.42 %
  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:  0.00 (0.32), residues: 682
  helix:  1.75 (0.27), residues: 312
  sheet: -0.80 (0.47), residues: 124
  loop : -1.92 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 184 
 TYR   0.010   0.001   TYR B 344 
 PHE   0.022   0.002   PHE A  39 
 TRP   0.006   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 7935)
  covalent geometry    : angle       0.57569 (11081)
  hydrogen bonds       : bond        0.05349 (  396)
  hydrogen bonds       : angle       4.31825 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 134
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7414 (tt0) cc_final: 0.5864 (tt0)
REVERT: A  134 LYS cc_start: 0.7443 (mmtt) cc_final: 0.7177 (mmtt)
REVERT: A  136 ASP cc_start: 0.7464 (p0) cc_final: 0.7214 (p0)
REVERT: A  184 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7472 (mtm-85)
REVERT: A  214 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8204 (ptpt)
REVERT: A  263 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7551 (ttm170)
REVERT: A  280 LYS cc_start: 0.8030 (mttt) cc_final: 0.7730 (ttmm)
REVERT: A  284 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7669 (ttmt)
REVERT: B   57 ASP cc_start: 0.6894 (m-30) cc_final: 0.6622 (m-30)
REVERT: B   91 VAL cc_start: 0.7917 (t) cc_final: 0.7693 (p)
REVERT: B  100 MET cc_start: 0.4577 (tpt) cc_final: 0.3747 (tpt)
REVERT: B  113 ILE cc_start: 0.7826 (mt) cc_final: 0.7610 (mt)
REVERT: B  139 PHE cc_start: 0.7772 (p90) cc_final: 0.7303 (p90)
REVERT: B  146 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5902 (tt)
REVERT: B  198 GLN cc_start: 0.7429 (tm-30) cc_final: 0.6937 (tm-30)
REVERT: B  232 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6843 (mm-30)
REVERT: B  241 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7725 (tmtt)
REVERT: B  342 TRP cc_start: 0.8467 (m100) cc_final: 0.8261 (m100)
  outliers start: 45
  outliers final: 26
  residues processed: 158
  average time/residue: 0.1369
  time to fit residues: 26.6677
Evaluate side-chains
  163 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 LYS
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  351 ILE
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 59 optimal weight:   40.0000
   chunk 4 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.184434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.151641 restraints weight = 11115.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 2.34
r_work: 0.3735 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7935  Z= 0.186
  Angle     :  0.529  11.089  11081  Z= 0.276
  Chirality :  0.038   0.192   1284
  Planarity :  0.004   0.042   1057
  Dihedral  : 18.823 163.129   2126
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.99 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 24.27 %
    Favored  : 68.61 %
  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:  0.09 (0.32), residues: 682
  helix:  1.83 (0.27), residues: 312
  sheet: -0.81 (0.46), residues: 130
  loop : -1.87 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 184 
 TYR   0.010   0.001   TYR B 344 
 PHE   0.018   0.002   PHE A 139 
 TRP   0.005   0.001   TRP A 206 
 HIS   0.007   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7935)
  covalent geometry    : angle       0.52861 (11081)
  hydrogen bonds       : bond        0.05024 (  396)
  hydrogen bonds       : angle       4.16155 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 132
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7472 (tt0) cc_final: 0.5929 (tt0)
REVERT: A  134 LYS cc_start: 0.7448 (mmtt) cc_final: 0.7170 (mmtt)
REVERT: A  136 ASP cc_start: 0.7475 (p0) cc_final: 0.7225 (p0)
REVERT: A  184 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7232 (mtp85)
REVERT: A  214 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8183 (ptpt)
REVERT: A  263 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7532 (ttm170)
REVERT: A  280 LYS cc_start: 0.8089 (mttt) cc_final: 0.7869 (ttmt)
REVERT: A  284 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7654 (ttmt)
REVERT: B   57 ASP cc_start: 0.6893 (m-30) cc_final: 0.6636 (m-30)
REVERT: B   91 VAL cc_start: 0.7903 (t) cc_final: 0.7676 (p)
REVERT: B  113 ILE cc_start: 0.7832 (mt) cc_final: 0.7631 (mt)
REVERT: B  139 PHE cc_start: 0.7738 (p90) cc_final: 0.7291 (p90)
REVERT: B  197 ILE cc_start: 0.8200 (mm) cc_final: 0.7901 (mp)
REVERT: B  198 GLN cc_start: 0.7423 (tm-30) cc_final: 0.7011 (tm-30)
REVERT: B  232 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6810 (mm-30)
REVERT: B  241 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7760 (tmtt)
REVERT: B  342 TRP cc_start: 0.8484 (m100) cc_final: 0.8263 (m100)
  outliers start: 44
  outliers final: 27
  residues processed: 155
  average time/residue: 0.1273
  time to fit residues: 24.3127
Evaluate side-chains
  158 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  125 LYS
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 LYS
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B   8 HIS
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** 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 = 0.4266 r_free = 0.4266 target = 0.185287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.152482 restraints weight = 10983.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 2.33
r_work: 0.3742 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7935  Z= 0.160
  Angle     :  0.506  10.889  11081  Z= 0.264
  Chirality :  0.037   0.194   1284
  Planarity :  0.003   0.039   1057
  Dihedral  : 18.793 163.167   2125
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.40 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 24.76 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.32), residues: 682
  helix:  1.92 (0.27), residues: 312
  sheet: -0.69 (0.48), residues: 130
  loop : -1.80 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 263 
 TYR   0.010   0.001   TYR B 344 
 PHE   0.017   0.002   PHE A 139 
 TRP   0.004   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7935)
  covalent geometry    : angle       0.50552 (11081)
  hydrogen bonds       : bond        0.04847 (  396)
  hydrogen bonds       : angle       4.02753 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 129
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7445 (tt0) cc_final: 0.5915 (tt0)
REVERT: A  134 LYS cc_start: 0.7434 (mmtt) cc_final: 0.7164 (mmtt)
REVERT: A  136 ASP cc_start: 0.7468 (p0) cc_final: 0.7221 (p0)
REVERT: A  184 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7413 (ttm170)
REVERT: A  214 LYS cc_start: 0.8490 (ptpt) cc_final: 0.8169 (ptpt)
REVERT: A  280 LYS cc_start: 0.8150 (mttt) cc_final: 0.7930 (ttmt)
REVERT: B   57 ASP cc_start: 0.6881 (m-30) cc_final: 0.6632 (m-30)
REVERT: B   91 VAL cc_start: 0.7906 (t) cc_final: 0.7684 (p)
REVERT: B  113 ILE cc_start: 0.7807 (mt) cc_final: 0.7602 (mt)
REVERT: B  139 PHE cc_start: 0.7682 (p90) cc_final: 0.7256 (p90)
REVERT: B  198 GLN cc_start: 0.7441 (tm-30) cc_final: 0.7009 (tm-30)
REVERT: B  232 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6795 (mm-30)
REVERT: B  241 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7707 (tmtt)
REVERT: B  342 TRP cc_start: 0.8480 (m100) cc_final: 0.8157 (m100)
  outliers start: 43
  outliers final: 33
  residues processed: 150
  average time/residue: 0.1251
  time to fit residues: 23.4934
Evaluate side-chains
  163 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  125 LYS
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  323 MET
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 PHE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   chunk 9 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 59 optimal weight:   40.0000
   chunk 43 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 242 ASN
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** 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 = 0.4261 r_free = 0.4261 target = 0.184681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.151740 restraints weight = 11026.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 2.33
r_work: 0.3737 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7935  Z= 0.178
  Angle     :  0.517  10.755  11081  Z= 0.270
  Chirality :  0.038   0.205   1284
  Planarity :  0.004   0.040   1057
  Dihedral  : 18.799 163.755   2121
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.13 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  7.44 %
    Allowed  : 24.11 %
    Favored  : 68.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.32), residues: 682
  helix:  1.92 (0.27), residues: 312
  sheet: -0.77 (0.47), residues: 130
  loop : -1.74 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 263 
 TYR   0.009   0.001   TYR B 344 
 PHE   0.018   0.002   PHE A 139 
 TRP   0.005   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7935)
  covalent geometry    : angle       0.51707 (11081)
  hydrogen bonds       : bond        0.04903 (  396)
  hydrogen bonds       : angle       4.01866 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 131
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7477 (tt0) cc_final: 0.5964 (tt0)
REVERT: A  134 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7163 (mmtt)
REVERT: A  136 ASP cc_start: 0.7476 (p0) cc_final: 0.7227 (p0)
REVERT: A  184 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7464 (mtm-85)
REVERT: A  214 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8170 (ptpt)
REVERT: B   57 ASP cc_start: 0.6902 (m-30) cc_final: 0.6660 (m-30)
REVERT: B   91 VAL cc_start: 0.7864 (t) cc_final: 0.7655 (p)
REVERT: B  139 PHE cc_start: 0.7649 (p90) cc_final: 0.7253 (p90)
REVERT: B  180 MET cc_start: 0.7358 (ttp) cc_final: 0.7123 (ttp)
REVERT: B  198 GLN cc_start: 0.7459 (tm-30) cc_final: 0.7047 (tm-30)
REVERT: B  232 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6788 (mm-30)
REVERT: B  241 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7726 (tmtt)
REVERT: B  342 TRP cc_start: 0.8518 (m100) cc_final: 0.8022 (m100)
  outliers start: 46
  outliers final: 32
  residues processed: 153
  average time/residue: 0.1412
  time to fit residues: 26.5518
Evaluate side-chains
  158 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 124
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 47 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0870
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.5762

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

Flipped N/Q/H residues before XYZ refinement:
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.183047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.150020 restraints weight = 10908.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 2.35
r_work: 0.3707 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7935  Z= 0.249
  Angle     :  0.581  10.633  11081  Z= 0.304
  Chirality :  0.041   0.221   1284
  Planarity :  0.004   0.041   1057
  Dihedral  : 18.905 164.855   2121
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.28 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 24.76 %
    Favored  : 68.93 %
  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: -0.05 (0.32), residues: 682
  helix:  1.68 (0.27), residues: 312
  sheet: -0.94 (0.46), residues: 130
  loop : -1.82 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 184 
 TYR   0.010   0.001   TYR B 254 
 PHE   0.023   0.002   PHE A 139 
 TRP   0.007   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 7935)
  covalent geometry    : angle       0.58150 (11081)
  hydrogen bonds       : bond        0.05363 (  396)
  hydrogen bonds       : angle       4.20973 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 123
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7143 (ttmt)
REVERT: A   53 GLU cc_start: 0.7518 (tt0) cc_final: 0.5986 (tt0)
REVERT: A  134 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7201 (mmtt)
REVERT: A  136 ASP cc_start: 0.7452 (p0) cc_final: 0.7190 (p0)
REVERT: A  184 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7146 (mtp85)
REVERT: A  214 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8223 (ptpt)
REVERT: B   57 ASP cc_start: 0.6924 (m-30) cc_final: 0.6676 (m-30)
REVERT: B   91 VAL cc_start: 0.7863 (t) cc_final: 0.7663 (p)
REVERT: B  139 PHE cc_start: 0.7686 (p90) cc_final: 0.7328 (p90)
REVERT: B  198 GLN cc_start: 0.7464 (tm-30) cc_final: 0.7047 (tm-30)
REVERT: B  232 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6876 (mm-30)
REVERT: B  241 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7777 (tmtt)
REVERT: B  342 TRP cc_start: 0.8548 (m100) cc_final: 0.8127 (m100)
  outliers start: 39
  outliers final: 32
  residues processed: 142
  average time/residue: 0.1278
  time to fit residues: 22.8860
Evaluate side-chains
  156 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  303 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  349 THR
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 72 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.185875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.153058 restraints weight = 11047.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.32
r_work: 0.3745 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7935  Z= 0.153
  Angle     :  0.520  10.578  11081  Z= 0.271
  Chirality :  0.038   0.212   1284
  Planarity :  0.003   0.040   1057
  Dihedral  : 18.766 162.316   2121
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  4.99 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 25.89 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.32), residues: 682
  helix:  1.88 (0.27), residues: 313
  sheet: -0.85 (0.47), residues: 130
  loop : -1.71 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 184 
 TYR   0.011   0.001   TYR B 353 
 PHE   0.022   0.002   PHE B 311 
 TRP   0.004   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7935)
  covalent geometry    : angle       0.51982 (11081)
  hydrogen bonds       : bond        0.04832 (  396)
  hydrogen bonds       : angle       3.98122 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7453 (tt0) cc_final: 0.6514 (tp30)
REVERT: A  134 LYS cc_start: 0.7452 (mmtt) cc_final: 0.7172 (mmtt)
REVERT: A  136 ASP cc_start: 0.7421 (p0) cc_final: 0.7189 (p0)
REVERT: A  184 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7233 (mtp85)
REVERT: A  214 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8201 (ptpt)
REVERT: B   57 ASP cc_start: 0.6800 (m-30) cc_final: 0.6573 (m-30)
REVERT: B  139 PHE cc_start: 0.7710 (p90) cc_final: 0.7402 (p90)
REVERT: B  197 ILE cc_start: 0.8153 (mm) cc_final: 0.7865 (mp)
REVERT: B  198 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7008 (tm-30)
REVERT: B  232 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6711 (mm-30)
REVERT: B  241 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7692 (tmtt)
REVERT: B  342 TRP cc_start: 0.8539 (m100) cc_final: 0.7969 (m100)
  outliers start: 36
  outliers final: 29
  residues processed: 146
  average time/residue: 0.1162
  time to fit residues: 21.4349
Evaluate side-chains
  157 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  102 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  214 LYS
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.185482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.152635 restraints weight = 10998.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.32
r_work: 0.3748 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7935  Z= 0.158
  Angle     :  0.530  10.587  11081  Z= 0.277
  Chirality :  0.038   0.217   1284
  Planarity :  0.004   0.081   1057
  Dihedral  : 18.743 163.036   2121
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.57 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 26.38 %
    Favored  : 68.12 %
  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 (0.32), residues: 682
  helix:  1.86 (0.27), residues: 313
  sheet: -0.88 (0.46), residues: 130
  loop : -1.72 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG B 184 
 TYR   0.012   0.001   TYR B 353 
 PHE   0.017   0.002   PHE A 139 
 TRP   0.005   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7935)
  covalent geometry    : angle       0.53037 (11081)
  hydrogen bonds       : bond        0.04841 (  396)
  hydrogen bonds       : angle       4.00897 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.7476 (tt0) cc_final: 0.6013 (tt0)
REVERT: A  134 LYS cc_start: 0.7471 (mmtt) cc_final: 0.7179 (mmtt)
REVERT: A  136 ASP cc_start: 0.7481 (p0) cc_final: 0.7247 (p0)
REVERT: A  184 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7234 (mtp85)
REVERT: B   57 ASP cc_start: 0.6795 (m-30) cc_final: 0.6574 (m-30)
REVERT: B  139 PHE cc_start: 0.7691 (p90) cc_final: 0.7386 (p90)
REVERT: B  198 GLN cc_start: 0.7459 (tm-30) cc_final: 0.7044 (tm-30)
REVERT: B  241 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7707 (tmtt)
REVERT: B  342 TRP cc_start: 0.8545 (m100) cc_final: 0.7967 (m100)
  outliers start: 34
  outliers final: 29
  residues processed: 146
  average time/residue: 0.0952
  time to fit residues: 17.6529
Evaluate side-chains
  155 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue   59 PHE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  356 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.183062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.149913 restraints weight = 10966.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 2.36
r_work: 0.3707 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7935  Z= 0.253
  Angle     :  0.599  10.638  11081  Z= 0.315
  Chirality :  0.042   0.239   1284
  Planarity :  0.004   0.038   1057
  Dihedral  : 18.884 164.793   2120
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.72 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 27.83 %
    Favored  : 67.31 %
  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 (0.32), residues: 682
  helix:  1.59 (0.27), residues: 313
  sheet: -0.97 (0.46), residues: 130
  loop : -1.78 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 184 
 TYR   0.012   0.001   TYR B 353 
 PHE   0.047   0.002   PHE B 311 
 TRP   0.007   0.001   TRP A 206 
 HIS   0.008   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 7935)
  covalent geometry    : angle       0.59898 (11081)
  hydrogen bonds       : bond        0.05431 (  396)
  hydrogen bonds       : angle       4.20043 ( 1126)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7145 (ttmt)
REVERT: A   53 GLU cc_start: 0.7526 (tt0) cc_final: 0.6013 (tt0)
REVERT: A  134 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7195 (mmtt)
REVERT: A  136 ASP cc_start: 0.7494 (p0) cc_final: 0.7250 (p0)
REVERT: A  184 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7237 (mtp85)
REVERT: B   57 ASP cc_start: 0.6908 (m-30) cc_final: 0.6682 (m-30)
REVERT: B  139 PHE cc_start: 0.7710 (p90) cc_final: 0.7417 (p90)
REVERT: B  198 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7121 (tm-30)
REVERT: B  241 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7739 (tmtt)
REVERT: B  342 TRP cc_start: 0.8565 (m100) cc_final: 0.8008 (m100)
  outliers start: 30
  outliers final: 26
  residues processed: 142
  average time/residue: 0.1017
  time to fit residues: 18.3231
Evaluate side-chains
  152 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   39 PHE
Chi-restraints excluded: chain A residue   97 LYS
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  353 TYR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 PHE
Chi-restraints excluded: chain B residue   54 MET
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  249 LYS
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.186238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.153577 restraints weight = 10914.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 2.30
r_work: 0.3759 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7935  Z= 0.135
  Angle     :  0.522  10.503  11081  Z= 0.274
  Chirality :  0.038   0.212   1284
  Planarity :  0.003   0.039   1057
  Dihedral  : 18.720 162.004   2120
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.55 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 27.51 %
    Favored  : 67.80 %
  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:  0.17 (0.32), residues: 682
  helix:  1.87 (0.27), residues: 312
  sheet: -0.91 (0.46), residues: 130
  loop : -1.68 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 184 
 TYR   0.013   0.001   TYR B 353 
 PHE   0.014   0.001   PHE A 139 
 TRP   0.003   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 302 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7935)
  covalent geometry    : angle       0.52220 (11081)
  hydrogen bonds       : bond        0.04737 (  396)
  hydrogen bonds       : angle       3.96373 ( 1126)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1733.41 seconds
wall clock time: 30 minutes 31.73 seconds (1831.73 seconds total)