Starting phenix.real_space_refine
on Tue Feb 11 13:56:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d9k_27264/02_2025/8d9k_27264.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d9k_27264/02_2025/8d9k_27264.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d9k_27264/02_2025/8d9k_27264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d9k_27264/02_2025/8d9k_27264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d9k_27264/02_2025/8d9k_27264.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d9k_27264/02_2025/8d9k_27264.cif"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.006 sd=   0.030
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: 5
    Type Number    sf(0)   Gaussians
     P      65      5.49       5
     S      21      5.16       5
     C    3387      2.51       5
     N     993      2.21       5
     O    1242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5708
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1740
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 15, 'TRANS': 198}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2578
          Classifications: {'peptide': 332}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 321}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 1390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1390
          Classifications: {'RNA': 65}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 28, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 8, 'rna3p': 56}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 43
    residue:
      pdb=" N   TYR A  37 " occ=0.88
      ... (10 atoms not shown)
      pdb=" OH  TYR A  37 " occ=0.88
    residue:
      pdb=" N   GLU A  43 " occ=0.83
      ... (7 atoms not shown)
      pdb=" OE2 GLU A  43 " occ=0.83
    residue:
      pdb=" N   ASP A  45 " occ=0.96
      ... (6 atoms not shown)
      pdb=" OD2 ASP A  45 " occ=0.96
    residue:
      pdb=" N   TYR A  50 " occ=0.90
      ... (10 atoms not shown)
      pdb=" OH  TYR A  50 " occ=0.90
    residue:
      pdb=" N   GLU A  52 " occ=0.87
      ... (7 atoms not shown)
      pdb=" OE2 GLU A  52 " occ=0.87
    residue:
      pdb=" N   PHE A  53 " occ=0.93
      ... (9 atoms not shown)
      pdb=" CZ  PHE A  53 " occ=0.93
    residue:
      pdb=" N   PHE A  54 " occ=0.88
      ... (9 atoms not shown)
      pdb=" CZ  PHE A  54 " occ=0.88
    residue:
      pdb=" N   GLU A  79 " occ=0.85
      ... (7 atoms not shown)
      pdb=" OE2 GLU A  79 " occ=0.85
    residue:
      pdb=" N   LYS A 111 " occ=0.98
      ... (7 atoms not shown)
      pdb=" NZ  LYS A 111 " occ=0.98
    residue:
      pdb=" N   ARG A 121 " occ=0.88
      ... (9 atoms not shown)
      pdb=" NH2 ARG A 121 " occ=0.88
    residue:
      pdb=" N   ARG A 138 " occ=0.99
      ... (9 atoms not shown)
      pdb=" NH2 ARG A 138 " occ=0.99
    residue:
      pdb=" N   MET A 142 " occ=0.86
      ... (6 atoms not shown)
      pdb=" CE  MET A 142 " occ=0.86
    ... (remaining 31 not shown)
  Time building chain proxies: 3.96, per 1000 atoms: 0.69
  Number of scatterers: 5708
  At special positions: 0
  Unit cell: (64.74, 100.845, 110.805, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      21     16.00
     P      65     15.00
     O    1242      8.00
     N     993      7.00
     C    3387      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.38
  Conformation dependent library (CDL) restraints added in 749.2 milliseconds
  

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1016

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 8 sheets defined
      22.7% alpha, 31.9% beta
      27 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 2.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 88 through 95
    Processing helix  chain 'A' and resid 109 through 126
    Processing helix  chain 'A' and resid 140 through 149
      removed outlier: 3.844A  pdb=" N   LEU A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
      Proline residue:  A 146  - end of helix
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.629A  pdb=" N   ALA A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU A 183 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 214
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 4.069A  pdb=" N   SER A 226 " --> pdb=" O   GLU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 238
      removed outlier: 3.728A  pdb=" N   HIS A 233 " --> pdb=" O   PRO A 229 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLY A 235 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   THR A 236 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   THR A 238 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 248
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.604A  pdb=" N   GLN B 233 " --> pdb=" O   LEU B 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 229 through 233'
    Processing helix  chain 'B' and resid 330 through 343
    Processing helix  chain 'B' and resid 343 through 348
      removed outlier: 4.398A  pdb=" N   LEU B 347 " --> pdb=" O   ASN B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 359
      removed outlier: 3.975A  pdb=" N   SER B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 362
      No H-bonds generated for 'chain 'B' and resid 360 through 362'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 138
      removed outlier: 5.498A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 7.753A  pdb=" N   LEU A 104 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   PHE A  80 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   LEU A 106 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ASP A  82 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   GLU A  79 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   MET A 157 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA A  81 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   PHE A 159 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ILE A  83 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   THR A 155 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   TYR A 195 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   MET A 157 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 8.186A  pdb=" N   ILE A 197 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   PHE A 159 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   GLY A 192 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 10
    Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 69
      removed outlier: 6.463A  pdb=" N   LEU B  85 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   VAL B  98 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU B  87 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 3.655A  pdb=" N   ALA B 107 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ASP B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL B 126 " --> pdb=" O   GLU B 141 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153
      removed outlier: 3.951A  pdb=" N   ASP B 150 " --> pdb=" O   ALA B 163 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE B 169 " --> pdb=" O   CYS B 184 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   TRP B 173 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ILE B 180 " --> pdb=" O   TRP B 173 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 196
      removed outlier: 3.854A  pdb=" N   ARG B 193 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   THR B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   LEU B 213 " --> pdb=" O   CYS B 226 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   CYS B 226 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU B 215 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 252
      removed outlier: 3.836A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   CYS B 262 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   VAL B 267 " --> pdb=" O   CYS B 262 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   GLN B 272 " --> pdb=" O   TYR B 282 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   TYR B 282 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ASP B 274 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   LEU B 280 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 298
      removed outlier: 3.981A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)

    155 hydrogen bonds defined for protein.
    426 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      69 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      29 stacking parallelities
  Total time for adding SS restraints: 2.07

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1574
        1.34 -     1.45: 1394
        1.45 -     1.57: 2850
        1.57 -     1.69: 128
        1.69 -     1.81: 27
  Bond restraints: 5973
  Sorted by residual:
  bond pdb=" CG  PRO B  92 "
       pdb=" CD  PRO B  92 "
    ideal  model  delta    sigma   weight residual
    1.512  1.492  0.020 2.70e-02 1.37e+03 5.36e-01
  bond pdb=" N   PHE A 166 "
       pdb=" CA  PHE A 166 "
    ideal  model  delta    sigma   weight residual
    1.462  1.472 -0.010 1.54e-02 4.22e+03 4.02e-01
  bond pdb=" CA  PHE A 166 "
       pdb=" CB  PHE A 166 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.54e-02 4.22e+03 3.50e-01
  bond pdb=" N   GLU B 114 "
       pdb=" CA  GLU B 114 "
    ideal  model  delta    sigma   weight residual
    1.461  1.470 -0.009 1.52e-02 4.33e+03 3.14e-01
  bond pdb=" CA  GLU B 167 "
       pdb=" CB  GLU B 167 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.69e-02 3.50e+03 2.79e-01
  ... (remaining 5968 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 8254
        1.01 -     2.02: 108
        2.02 -     3.03: 37
        3.03 -     4.04: 5
        4.04 -     5.06: 4
  Bond angle restraints: 8408
  Sorted by residual:
  angle pdb=" C   TYR B 361 "
        pdb=" N   LYS B 362 "
        pdb=" CA  LYS B 362 "
      ideal   model   delta    sigma   weight residual
     121.70  126.76   -5.06 1.80e+00 3.09e-01 7.89e+00
  angle pdb=" C   ASP B 166 "
        pdb=" N   GLU B 167 "
        pdb=" CA  GLU B 167 "
      ideal   model   delta    sigma   weight residual
     121.54  125.67   -4.13 1.91e+00 2.74e-01 4.68e+00
  angle pdb=" C   SER B 113 "
        pdb=" N   GLU B 114 "
        pdb=" CA  GLU B 114 "
      ideal   model   delta    sigma   weight residual
     122.07  124.77   -2.70 1.43e+00 4.89e-01 3.57e+00
  angle pdb=" C   HIS A 165 "
        pdb=" N   PHE A 166 "
        pdb=" CA  PHE A 166 "
      ideal   model   delta    sigma   weight residual
     122.08  124.50   -2.42 1.47e+00 4.63e-01 2.71e+00
  angle pdb=" CA  GLU B 167 "
        pdb=" CB  GLU B 167 "
        pdb=" CG  GLU B 167 "
      ideal   model   delta    sigma   weight residual
     114.10  117.33   -3.23 2.00e+00 2.50e-01 2.60e+00
  ... (remaining 8403 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.18: 3340
       19.18 -    38.35: 148
       38.35 -    57.53: 72
       57.53 -    76.70: 81
       76.70 -    95.88: 2
  Dihedral angle restraints: 3643
    sinusoidal: 2071
      harmonic: 1572
  Sorted by residual:
  dihedral pdb=" CA  LEU B  35 "
           pdb=" CB  LEU B  35 "
           pdb=" CG  LEU B  35 "
           pdb=" CD1 LEU B  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.67   45.33     3      1.50e+01 4.44e-03 8.15e+00
  dihedral pdb=" CA  LEU A 104 "
           pdb=" CB  LEU A 104 "
           pdb=" CG  LEU A 104 "
           pdb=" CD1 LEU A 104 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  140.47   39.53     3      1.50e+01 4.44e-03 7.01e+00
  dihedral pdb=" O4'   A C   7 "
           pdb=" C1'   A C   7 "
           pdb=" N9    A C   7 "
           pdb=" C4    A C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -142.86   36.86     1      1.70e+01 3.46e-03 6.64e+00
  ... (remaining 3640 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 687
       0.025 -    0.049: 181
       0.049 -    0.074: 52
       0.074 -    0.098: 33
       0.098 -    0.123: 36
  Chirality restraints: 989
  Sorted by residual:
  chirality pdb=" CA  VAL B  98 "
            pdb=" N   VAL B  98 "
            pdb=" C   VAL B  98 "
            pdb=" CB  VAL B  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.78e-01
  chirality pdb=" CA  ILE B 160 "
            pdb=" N   ILE B 160 "
            pdb=" C   ILE B 160 "
            pdb=" CB  ILE B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.71e-01
  chirality pdb=" CA  VAL B  16 "
            pdb=" N   VAL B  16 "
            pdb=" C   VAL B  16 "
            pdb=" CB  VAL B  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.64e-01
  ... (remaining 986 not shown)

  Planarity restraints: 831
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  59 "   -0.013 2.00e-02 2.50e+03   6.11e-03 1.12e+00
        pdb=" N9    G C  59 "    0.015 2.00e-02 2.50e+03
        pdb=" C8    G C  59 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G C  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  59 "    0.002 2.00e-02 2.50e+03
        pdb=" O6    G C  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    G C  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G C  59 "    0.000 2.00e-02 2.50e+03
        pdb=" N2    G C  59 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C  59 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    G C  59 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 228 "   -0.016 5.00e-02 4.00e+02   2.39e-02 9.11e-01
        pdb=" N   PRO A 229 "    0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO A 229 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 229 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 318 "   -0.015 5.00e-02 4.00e+02   2.23e-02 7.97e-01
        pdb=" N   PRO B 319 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO B 319 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 319 "   -0.012 5.00e-02 4.00e+02
  ... (remaining 828 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1350
        2.80 -     3.32: 5002
        3.32 -     3.85: 10049
        3.85 -     4.37: 11700
        4.37 -     4.90: 18273
  Nonbonded interactions: 46374
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS B 187 "
            pdb=" OG  SER B 208 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OG  SER B 146 "
            pdb=" OD2 ASP B 166 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OP1   U C  60 "
            pdb=" N4    C C  61 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O6    G C  10 "
            pdb=" N2    G C  45 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" OG1 THR B 188 "
            pdb=" OD2 ASP B 210 "
     model   vdw
     2.311 3.040
  ... (remaining 46369 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.170
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.450
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
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      :  0.001   0.020   5973  Z= 0.082
  Angle     :  0.366   5.055   8408  Z= 0.182
  Chirality :  0.034   0.123    989
  Planarity :  0.002   0.024    831
  Dihedral  : 16.349  95.877   2627
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  5.77 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.38), residues: 534
  helix:  1.29 (0.58), residues: 103
  sheet:  1.77 (0.39), residues: 185
  loop :  0.37 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 206 
 HIS   0.002   0.000   HIS A 210 
 PHE   0.009   0.001   PHE A 166 
 TYR   0.004   0.001   TYR B 361 
 ARG   0.002   0.000   ARG B 318 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9241 (t) cc_final: 0.8861 (p)
REVERT: A  114 ASP cc_start: 0.9260 (t0) cc_final: 0.9017 (t0)
REVERT: A  115 TYR cc_start: 0.9439 (t80) cc_final: 0.8910 (t80)
REVERT: A  118 ASP cc_start: 0.9329 (m-30) cc_final: 0.9065 (m-30)
REVERT: A  175 ILE cc_start: 0.9475 (mt) cc_final: 0.9115 (tp)
REVERT: B   71 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8744 (tppt)
REVERT: B  122 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8545 (ttpp)
  outliers start: 3
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1989
  time to fit residues: 13.4622
Evaluate side-chains
  20 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 54 optimal weight:   20.0000
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 147 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.047010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.034465 restraints weight = 32413.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.035549 restraints weight = 15686.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.036268 restraints weight = 10059.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2722
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2722 r_free = 0.2722    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5973  Z= 0.282
  Angle     :  0.531   5.816   8408  Z= 0.269
  Chirality :  0.038   0.132    989
  Planarity :  0.003   0.018    831
  Dihedral  : 19.223  95.935   1620
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  8.55 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.38), residues: 534
  helix:  1.53 (0.57), residues: 97
  sheet:  1.70 (0.39), residues: 179
  loop :  0.29 (0.42), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B 187 
 PHE   0.010   0.001   PHE A 166 
 TYR   0.007   0.001   TYR A 150 
 ARG   0.003   0.000   ARG B 248 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 21
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 TYR cc_start: 0.9530 (t80) cc_final: 0.9301 (t80)
REVERT: A  147 ASN cc_start: 0.9594 (m110) cc_final: 0.9360 (m-40)
REVERT: A  175 ILE cc_start: 0.9584 (mt) cc_final: 0.9256 (tp)
REVERT: B   71 LYS cc_start: 0.9315 (tmtt) cc_final: 0.9066 (tppt)
REVERT: B   87 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8681 (tt)
REVERT: B  122 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8499 (ttpt)
REVERT: B  147 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8666 (ptp)
  outliers start: 9
  outliers final: 2
  residues processed: 28
  average time/residue: 0.2065
  time to fit residues: 7.8873
Evaluate side-chains
  23 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  192 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 31 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   overall best weight:    3.5188

-------------------------------------------------------------------------------
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 = 0.3100 r_free = 0.3100 target = 0.045103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.032573 restraints weight = 32830.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.033635 restraints weight = 15464.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.034346 restraints weight = 9939.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5973  Z= 0.231
  Angle     :  0.471   4.687   8408  Z= 0.243
  Chirality :  0.037   0.159    989
  Planarity :  0.003   0.021    831
  Dihedral  : 19.166  94.664   1620
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  9.19 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.38), residues: 534
  helix:  1.98 (0.57), residues: 91
  sheet:  1.47 (0.39), residues: 179
  loop :  0.10 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 206 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.011   0.001   PHE A 166 
 TYR   0.006   0.001   TYR A 150 
 ARG   0.004   0.000   ARG B 341 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9263 (t) cc_final: 0.8954 (p)
REVERT: A  115 TYR cc_start: 0.9575 (t80) cc_final: 0.9037 (t80)
REVERT: A  175 ILE cc_start: 0.9586 (mt) cc_final: 0.9251 (tp)
REVERT: B   71 LYS cc_start: 0.9420 (tmtt) cc_final: 0.9156 (tppt)
REVERT: B   87 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8731 (tt)
  outliers start: 7
  outliers final: 1
  residues processed: 25
  average time/residue: 0.2139
  time to fit residues: 7.3856
Evaluate side-chains
  17 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain B residue   87 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 45 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 55 optimal weight:   20.0000
   chunk 18 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    4.9988

-------------------------------------------------------------------------------
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 = 0.3055 r_free = 0.3055 target = 0.043558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.031166 restraints weight = 33920.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.032211 restraints weight = 15871.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.032869 restraints weight = 10183.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5973  Z= 0.330
  Angle     :  0.553   4.950   8408  Z= 0.281
  Chirality :  0.039   0.192    989
  Planarity :  0.003   0.027    831
  Dihedral  : 19.312  98.080   1620
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.40 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.38), residues: 534
  helix:  1.84 (0.57), residues: 94
  sheet:  1.33 (0.39), residues: 176
  loop : -0.31 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 206 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.010   0.001   PHE B 271 
 TYR   0.006   0.001   TYR A  50 
 ARG   0.003   0.000   ARG B  99 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 17
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9359 (t) cc_final: 0.9054 (p)
REVERT: A  115 TYR cc_start: 0.9578 (t80) cc_final: 0.9067 (t80)
REVERT: A  175 ILE cc_start: 0.9590 (mt) cc_final: 0.9289 (tp)
REVERT: B   71 LYS cc_start: 0.9467 (tmtt) cc_final: 0.9239 (tppt)
REVERT: B   87 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8791 (tt)
REVERT: B  122 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8388 (ptmt)
  outliers start: 10
  outliers final: 4
  residues processed: 26
  average time/residue: 0.2344
  time to fit residues: 8.1427
Evaluate side-chains
  20 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 15
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  249 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    4.5588

-------------------------------------------------------------------------------
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 = 0.3052 r_free = 0.3052 target = 0.043284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.030985 restraints weight = 33664.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.032015 restraints weight = 15899.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.032705 restraints weight = 10240.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5973  Z= 0.291
  Angle     :  0.506   4.768   8408  Z= 0.261
  Chirality :  0.038   0.211    989
  Planarity :  0.003   0.031    831
  Dihedral  : 19.367  96.698   1620
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  8.97 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.38), residues: 534
  helix:  1.56 (0.56), residues: 97
  sheet:  1.20 (0.38), residues: 177
  loop : -0.34 (0.41), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 216 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.011   0.001   PHE A 166 
 TYR   0.005   0.001   TYR A  50 
 ARG   0.003   0.000   ARG B  99 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 17
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9306 (t) cc_final: 0.9012 (p)
REVERT: A  115 TYR cc_start: 0.9565 (t80) cc_final: 0.9093 (t80)
REVERT: A  175 ILE cc_start: 0.9601 (mt) cc_final: 0.9290 (tp)
REVERT: B   87 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8776 (tt)
  outliers start: 9
  outliers final: 5
  residues processed: 26
  average time/residue: 0.2132
  time to fit residues: 7.6422
Evaluate side-chains
  22 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 16
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  249 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 7 optimal weight:    9.9990
   chunk 32 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 54 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0980
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3127 r_free = 0.3127 target = 0.045434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.033144 restraints weight = 32586.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.034196 restraints weight = 15761.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.034918 restraints weight = 10145.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5973  Z= 0.112
  Angle     :  0.435   8.022   8408  Z= 0.221
  Chirality :  0.037   0.200    989
  Planarity :  0.003   0.028    831
  Dihedral  : 19.151  94.823   1620
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  9.83 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.38), residues: 534
  helix:  1.69 (0.57), residues: 97
  sheet:  1.42 (0.39), residues: 170
  loop : -0.32 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 173 
 HIS   0.004   0.001   HIS B 144 
 PHE   0.012   0.001   PHE A 166 
 TYR   0.003   0.000   TYR A 150 
 ARG   0.002   0.000   ARG A 119 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9119 (t) cc_final: 0.8865 (p)
REVERT: A  115 TYR cc_start: 0.9523 (t80) cc_final: 0.9317 (t80)
REVERT: A  147 ASN cc_start: 0.9514 (m110) cc_final: 0.9262 (m-40)
REVERT: A  175 ILE cc_start: 0.9551 (mt) cc_final: 0.9207 (tp)
REVERT: B  122 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8652 (ptpt)
  outliers start: 3
  outliers final: 2
  residues processed: 25
  average time/residue: 0.2128
  time to fit residues: 7.1856
Evaluate side-chains
  21 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue  200 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 56 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3082 r_free = 0.3082 target = 0.044049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.031270 restraints weight = 34506.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.032311 restraints weight = 16490.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.033026 restraints weight = 10672.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5973  Z= 0.281
  Angle     :  0.513   8.957   8408  Z= 0.258
  Chirality :  0.038   0.200    989
  Planarity :  0.003   0.032    831
  Dihedral  : 19.203  96.656   1620
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.62 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.38), residues: 534
  helix:  1.64 (0.56), residues: 97
  sheet:  1.31 (0.39), residues: 169
  loop : -0.37 (0.40), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.011   0.001   PHE A 166 
 TYR   0.014   0.001   TYR B  38 
 ARG   0.003   0.000   ARG B  99 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A   95 SER cc_start: 0.9363 (t) cc_final: 0.8993 (p)
REVERT: A  115 TYR cc_start: 0.9603 (t80) cc_final: 0.9386 (t80)
REVERT: A  175 ILE cc_start: 0.9579 (mt) cc_final: 0.9242 (tp)
REVERT: B  122 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8660 (ptpt)
REVERT: B  200 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7974 (mp10)
  outliers start: 8
  outliers final: 4
  residues processed: 27
  average time/residue: 0.2162
  time to fit residues: 7.9246
Evaluate side-chains
  23 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 52 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 41 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 58 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   overall best weight:    4.3188

-------------------------------------------------------------------------------
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 = 0.3077 r_free = 0.3077 target = 0.043839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.031117 restraints weight = 33793.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.032148 restraints weight = 16299.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.032832 restraints weight = 10594.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5973  Z= 0.278
  Angle     :  0.535   8.687   8408  Z= 0.266
  Chirality :  0.038   0.204    989
  Planarity :  0.003   0.032    831
  Dihedral  : 19.285  97.111   1620
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.04 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.37), residues: 534
  helix:  1.54 (0.57), residues: 94
  sheet:  1.14 (0.38), residues: 171
  loop : -0.42 (0.40), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.012   0.001   PHE A 166 
 TYR   0.005   0.001   TYR A  50 
 ARG   0.002   0.000   ARG B  99 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9286 (t) cc_final: 0.9010 (p)
REVERT: A  115 TYR cc_start: 0.9566 (t80) cc_final: 0.9363 (t80)
REVERT: A  175 ILE cc_start: 0.9530 (mt) cc_final: 0.9160 (tp)
REVERT: B  122 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8722 (ptpt)
REVERT: B  200 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7998 (mp10)
  outliers start: 7
  outliers final: 5
  residues processed: 27
  average time/residue: 0.2073
  time to fit residues: 7.6919
Evaluate side-chains
  25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3096 r_free = 0.3096 target = 0.044260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.031892 restraints weight = 33287.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.032907 restraints weight = 16004.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.033620 restraints weight = 10399.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5973  Z= 0.193
  Angle     :  0.489   8.931   8408  Z= 0.244
  Chirality :  0.037   0.201    989
  Planarity :  0.003   0.029    831
  Dihedral  : 19.206  96.099   1620
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.04 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.37), residues: 534
  helix:  1.63 (0.57), residues: 97
  sheet:  1.25 (0.38), residues: 169
  loop : -0.43 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.011   0.001   PHE A 166 
 TYR   0.007   0.001   TYR B  38 
 ARG   0.002   0.000   ARG B 214 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9225 (t) cc_final: 0.8936 (p)
REVERT: A  175 ILE cc_start: 0.9537 (mt) cc_final: 0.9170 (tp)
REVERT: B  122 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8674 (ptpt)
  outliers start: 7
  outliers final: 6
  residues processed: 27
  average time/residue: 0.2055
  time to fit residues: 7.6597
Evaluate side-chains
  26 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  249 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0980
   chunk 8 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 57 optimal weight:   20.0000
   chunk 43 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 147 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.044998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.032813 restraints weight = 32771.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.033874 restraints weight = 15762.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.034589 restraints weight = 10053.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2699 r_free = 0.2699    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.033         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5973  Z= 0.147
  Angle     :  0.481   8.775   8408  Z= 0.237
  Chirality :  0.037   0.191    989
  Planarity :  0.003   0.028    831
  Dihedral  : 19.115  95.087   1620
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.04 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.37), residues: 534
  helix:  1.62 (0.56), residues: 97
  sheet:  1.20 (0.39), residues: 171
  loop : -0.37 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 144 
 PHE   0.012   0.001   PHE A 166 
 TYR   0.015   0.001   TYR A 115 
 ARG   0.004   0.000   ARG B  21 

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

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

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1068 Ramachandran restraints generated.
    534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 SER cc_start: 0.9140 (t) cc_final: 0.8901 (p)
REVERT: B  122 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8822 (ptpt)
REVERT: B  346 MET cc_start: 0.9088 (mmm) cc_final: 0.8727 (tpp)
  outliers start: 7
  outliers final: 7
  residues processed: 28
  average time/residue: 0.2014
  time to fit residues: 7.5777
Evaluate side-chains
  27 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 20
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  200 GLN
Chi-restraints excluded: chain B residue  249 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 147 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.043629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.031259 restraints weight = 34142.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.032271 restraints weight = 16641.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.032974 restraints weight = 10890.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.4148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   5973  Z= 0.271
  Angle     :  0.532   8.469   8408  Z= 0.264
  Chirality :  0.038   0.183    989
  Planarity :  0.003   0.030    831
  Dihedral  : 19.225  96.494   1620
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  :  9.40 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.37), residues: 534
  helix:  1.53 (0.56), residues: 97
  sheet:  1.05 (0.38), residues: 171
  loop : -0.45 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.010   0.001   PHE A 166 
 TYR   0.009   0.001   TYR B  38 
 ARG   0.002   0.000   ARG B  99 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1576.92 seconds
wall clock time: 29 minutes 8.78 seconds (1748.78 seconds total)