Starting phenix.real_space_refine
on Fri Sep 11 06:44:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/24vn_69845/09_2026/24vn_69845.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/24vn_69845/09_2026/24vn_69845.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/24vn_69845/09_2026/24vn_69845.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/24vn_69845/09_2026/24vn_69845.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/24vn_69845/09_2026/24vn_69845.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/24vn_69845/09_2026/24vn_69845.cif"
  }
  resolution = 3.58
  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=   0.010 sd=   0.086
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       2      5.49       5
     S      38      5.16       5
     C    5361      2.51       5
     N    1296      2.21       5
     O    1359      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8056
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1913
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 5, 'TRANS': 233}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1913
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 5, 'TRANS': 233}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1982
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 4, 'TRANS': 238}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 2006
          Classifications: {'peptide': 247}
          Link IDs: {'PTRANS': 4, 'TRANS': 242}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'9PE': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'9PE': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 81
          Unusual residues: {'YJ0': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 81
          Unusual residues: {'YJ0': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.92, per 1000 atoms: 0.24
  Number of scatterers: 8056
  At special positions: 0
  Unit cell: (116.309, 127.179, 82.612, 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      38     16.00
     P       2     15.00
     O    1359      8.00
     N    1296      7.00
     C    5361      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: 0.66
  Conformation dependent library (CDL) restraints added in 426.5 milliseconds
  

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1780

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 0 sheets defined
      79.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 112 through 117
    Processing helix  chain 'A' and resid 124 through 143
      removed outlier: 4.004A  pdb=" N   LEU A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 142 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 178
      removed outlier: 3.878A  pdb=" N   TRP A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 196
      removed outlier: 3.975A  pdb=" N   LYS A 196 " --> pdb=" O   LYS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 208
    Processing helix  chain 'A' and resid 230 through 239
    Processing helix  chain 'A' and resid 244 through 257
      removed outlier: 3.516A  pdb=" N   LEU A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   HIS A 257 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 283
    Processing helix  chain 'A' and resid 302 through 315
    Processing helix  chain 'A' and resid 327 through 345
      removed outlier: 3.644A  pdb=" N   LEU A 331 " --> pdb=" O   TRP A 327 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ILE A 332 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA A 333 " --> pdb=" O   GLY A 329 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ALA A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 366
      removed outlier: 3.768A  pdb=" N   LEU A 351 " --> pdb=" O   PRO A 347 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   GLY A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 117
    Processing helix  chain 'C' and resid 123 through 143
    Processing helix  chain 'C' and resid 150 through 178
    Processing helix  chain 'C' and resid 188 through 196
      removed outlier: 3.889A  pdb=" N   LYS C 196 " --> pdb=" O   LYS C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 208
    Processing helix  chain 'C' and resid 230 through 239
    Processing helix  chain 'C' and resid 244 through 257
      removed outlier: 3.613A  pdb=" N   LEU C 250 " --> pdb=" O   THR C 246 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA C 256 " --> pdb=" O   SER C 252 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   HIS C 257 " --> pdb=" O   ALA C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 283
      removed outlier: 3.573A  pdb=" N   THR C 263 " --> pdb=" O   LYS C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 315
    Processing helix  chain 'C' and resid 327 through 345
      removed outlier: 3.651A  pdb=" N   LEU C 331 " --> pdb=" O   TRP C 327 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ILE C 332 " --> pdb=" O   GLU C 328 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA C 333 " --> pdb=" O   GLY C 329 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA C 345 " --> pdb=" O   VAL C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 346 through 366
      removed outlier: 3.751A  pdb=" N   LEU C 351 " --> pdb=" O   PRO C 347 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLY C 352 " --> pdb=" O   ALA C 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 85
    Processing helix  chain 'B' and resid 91 through 114
      removed outlier: 4.125A  pdb=" N   HIS B  95 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE B 114 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 147
    Processing helix  chain 'B' and resid 156 through 165
      removed outlier: 3.511A  pdb=" N   LEU B 160 " --> pdb=" O   TRP B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 182
    Processing helix  chain 'B' and resid 200 through 210
      removed outlier: 4.197A  pdb=" N   ILE B 204 " --> pdb=" O   ARG B 200 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   MET B 210 " --> pdb=" O   ARG B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 227
    Processing helix  chain 'B' and resid 227 through 253
      removed outlier: 3.890A  pdb=" N   VAL B 232 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 275
    Processing helix  chain 'B' and resid 286 through 305
      removed outlier: 3.709A  pdb=" N   ALA B 305 " --> pdb=" O   VAL B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 308
      No H-bonds generated for 'chain 'B' and resid 306 through 308'
    Processing helix  chain 'B' and resid 309 through 326
    Processing helix  chain 'D' and resid 71 through 85
    Processing helix  chain 'D' and resid 93 through 114
      removed outlier: 3.734A  pdb=" N   ILE D 114 " --> pdb=" O   VAL D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 145
    Processing helix  chain 'D' and resid 154 through 164
      removed outlier: 3.561A  pdb=" N   LEU D 160 " --> pdb=" O   TRP D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 183
    Processing helix  chain 'D' and resid 199 through 201
      No H-bonds generated for 'chain 'D' and resid 199 through 201'
    Processing helix  chain 'D' and resid 202 through 209
    Processing helix  chain 'D' and resid 214 through 227
    Processing helix  chain 'D' and resid 230 through 253
    Processing helix  chain 'D' and resid 262 through 275
    Processing helix  chain 'D' and resid 286 through 305
      removed outlier: 3.759A  pdb=" N   ALA D 305 " --> pdb=" O   VAL D 301 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 305 through 326
      removed outlier: 3.586A  pdb=" N   GLY D 309 " --> pdb=" O   ALA D 305 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER D 313 " --> pdb=" O   GLY D 309 " (cutoff:3.500A)

    547 hydrogen bonds defined for protein.
    1641 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1161
        1.31 -     1.43: 2449
        1.43 -     1.56: 4607
        1.56 -     1.68: 5
        1.68 -     1.81: 52
  Bond restraints: 8274
  Sorted by residual:
  bond pdb=" CA  GLU B 139 "
       pdb=" C   GLU B 139 "
    ideal  model  delta    sigma   weight residual
    1.524  1.465  0.059 1.24e-02 6.50e+03 2.25e+01
  bond pdb=" C31 9PE C1001 "
       pdb=" O31 9PE C1001 "
    ideal  model  delta    sigma   weight residual
    1.325  1.399 -0.074 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" C31 9PE A1001 "
       pdb=" O31 9PE A1001 "
    ideal  model  delta    sigma   weight residual
    1.325  1.399 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" C21 9PE A1001 "
       pdb=" O21 9PE A1001 "
    ideal  model  delta    sigma   weight residual
    1.329  1.399 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" C21 9PE C1001 "
       pdb=" O21 9PE C1001 "
    ideal  model  delta    sigma   weight residual
    1.329  1.398 -0.069 2.00e-02 2.50e+03 1.20e+01
  ... (remaining 8269 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 10927
        2.54 -     5.07: 195
        5.07 -     7.61: 69
        7.61 -    10.15: 20
       10.15 -    12.68: 6
  Bond angle restraints: 11217
  Sorted by residual:
  angle pdb=" N   ARG A 230 "
        pdb=" CA  ARG A 230 "
        pdb=" C   ARG A 230 "
      ideal   model   delta    sigma   weight residual
     114.56  108.71    5.85 1.27e+00 6.20e-01 2.12e+01
  angle pdb=" N   ARG C 230 "
        pdb=" CA  ARG C 230 "
        pdb=" C   ARG C 230 "
      ideal   model   delta    sigma   weight residual
     114.31  108.98    5.33 1.29e+00 6.01e-01 1.71e+01
  angle pdb=" O12 9PE A1001 "
        pdb=" P   9PE A1001 "
        pdb=" O14 9PE A1001 "
      ideal   model   delta    sigma   weight residual
     120.90  109.32   11.58 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" O12 9PE C1001 "
        pdb=" P   9PE C1001 "
        pdb=" O14 9PE C1001 "
      ideal   model   delta    sigma   weight residual
     120.90  109.56   11.34 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" C12 YJ0 B 901 "
        pdb=" C7  YJ0 B 901 "
        pdb=" C6  YJ0 B 901 "
      ideal   model   delta    sigma   weight residual
     118.64  129.75  -11.11 3.00e+00 1.11e-01 1.37e+01
  ... (remaining 11212 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.63: 4647
       35.63 -    71.25: 269
       71.25 -   106.88: 69
      106.88 -   142.50: 62
      142.50 -   178.13: 18
  Dihedral angle restraints: 5065
    sinusoidal: 2281
      harmonic: 2784
  Sorted by residual:
  dihedral pdb=" O30 YJ0 D 901 "
           pdb=" C31 YJ0 D 901 "
           pdb=" C32 YJ0 D 901 "
           pdb=" O52 YJ0 D 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     234.92   56.79  178.13     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O21 9PE A1001 "
           pdb=" C2  9PE A1001 "
           pdb=" C3  9PE A1001 "
           pdb=" O31 9PE A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     303.57  129.53  174.04     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O36 YJ0 D 901 "
           pdb=" C31 YJ0 D 901 "
           pdb=" C32 YJ0 D 901 "
           pdb=" O52 YJ0 D 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     124.08  -62.61 -173.31     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 5062 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.215: 1254
       1.215 -    2.430: 0
       2.430 -    3.645: 0
       3.645 -    4.861: 4
       4.861 -    6.076: 21
  Chirality restraints: 1279
  Sorted by residual:
  chirality pdb=" C12 YJ0 D 901 "
            pdb=" C11 YJ0 D 901 "
            pdb=" C13 YJ0 D 901 "
            pdb=" C7  YJ0 D 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      3.10   -2.98    6.08 2.00e-01 2.50e+01 9.23e+02
  chirality pdb=" C8  YJ0 B 901 "
            pdb=" C10 YJ0 B 901 "
            pdb=" C7  YJ0 B 901 "
            pdb=" O9  YJ0 B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.87    2.73   -5.60 2.00e-01 2.50e+01 7.84e+02
  chirality pdb=" C16 YJ0 D 901 "
            pdb=" C11 YJ0 D 901 "
            pdb=" C15 YJ0 D 901 "
            pdb=" C17 YJ0 D 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.82    2.75   -5.57 2.00e-01 2.50e+01 7.75e+02
  ... (remaining 1276 not shown)

  Planarity restraints: 1314
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C17 YJ0 D 901 "    0.102 2.00e-02 2.50e+03   8.46e-02 8.94e+01
        pdb=" C18 YJ0 D 901 "   -0.126 2.00e-02 2.50e+03
        pdb=" C19 YJ0 D 901 "   -0.049 2.00e-02 2.50e+03
        pdb=" C20 YJ0 D 901 "   -0.011 2.00e-02 2.50e+03
        pdb=" C24 YJ0 D 901 "    0.084 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D  86 "    0.036 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO D  87 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO D  87 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D  87 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 156 "    0.014 2.00e-02 2.50e+03   1.36e-02 4.66e+00
        pdb=" CG  TRP D 156 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 156 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 156 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 156 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 156 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 156 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 156 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 156 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 156 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1311 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 984
        2.75 -     3.29: 8210
        3.29 -     3.82: 13418
        3.82 -     4.36: 14394
        4.36 -     4.90: 24990
  Nonbonded interactions: 61996
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 193 "
            pdb=" NZ  LYS A 196 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OE2 GLU C 283 "
            pdb=" OG1 THR C 326 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OE2 GLU A 283 "
            pdb=" OG1 THR A 326 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OH  TYR C 319 "
            pdb=" OG1 THR B 273 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   LEU D 271 "
            pdb=" OG1 THR D 275 "
     model   vdw
     2.266 3.040
  ... (remaining 61991 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 'C'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and (resid 70 through 182 or resid 197 through 901))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.690
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
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   0.074   8274  Z= 0.240
  Angle     :  0.981  12.681  11217  Z= 0.458
  Chirality :  0.726   6.076   1279
  Planarity :  0.005   0.085   1314
  Dihedral  : 30.495 178.127   3285
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.35 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 30.92 %
    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:  1.17 (0.28), residues: 952
  helix:  1.81 (0.20), residues: 718
  sheet:  None (None), residues: 0
  loop : -2.65 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 324 
 TYR   0.031   0.001   TYR D  81 
 PHE   0.033   0.002   PHE C 193 
 TRP   0.037   0.001   TRP D 156 
 HIS   0.005   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00461 /  0.24 ( 8274)
  covalent geometry    : angle       0.98089 /  0.46 (11217)
  hydrogen bonds       : bond        0.12366 /  8.13 (  547)
  hydrogen bonds       : angle       5.18420 /  3.70 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 204
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7276 (ttm-80)
REVERT: D  139 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7697 (tm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 204
  average time/residue: 0.1055
  time to fit residues: 28.1930
Evaluate side-chains
  190 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 188
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 HIS
Chi-restraints excluded: chain A residue  151 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 325 GLN
** D  78 ASN ** 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 = 0.4232 r_free = 0.4232 target = 0.190119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.123263 restraints weight = 11539.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.123438 restraints weight = 8089.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.124425 restraints weight = 6115.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.124234 restraints weight = 4870.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.124330 restraints weight = 4657.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8274  Z= 0.183
  Angle     :  1.089  35.137  11217  Z= 0.443
  Chirality :  0.106   2.260   1279
  Planarity :  0.004   0.048   1314
  Dihedral  : 23.865 179.740   1541
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.62 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 26.18 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.29), residues: 952
  helix:  1.89 (0.20), residues: 729
  sheet:  None (None), residues: 0
  loop : -2.86 (0.40), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 239 
 TYR   0.023   0.001   TYR B 153 
 PHE   0.019   0.001   PHE C 171 
 TRP   0.019   0.001   TRP D 156 
 HIS   0.003   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.18 ( 8274)
  covalent geometry    : angle       1.08875 /  0.44 (11217)
  hydrogen bonds       : bond        0.05454 /  3.52 (  547)
  hydrogen bonds       : angle       4.47658 /  3.22 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 200
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 GLN cc_start: 0.8161 (mp10) cc_final: 0.7886 (mp10)
REVERT: C  146 LYS cc_start: 0.8144 (tppt) cc_final: 0.7491 (tppt)
REVERT: C  149 GLU cc_start: 0.7987 (pm20) cc_final: 0.7562 (pm20)
REVERT: C  233 GLN cc_start: 0.8026 (mp10) cc_final: 0.7754 (mp10)
REVERT: C  272 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8260 (tp)
REVERT: C  314 LEU cc_start: 0.8801 (mp) cc_final: 0.8444 (mt)
REVERT: B  152 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7761 (ttm-80)
REVERT: B  161 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8651 (mmtt)
REVERT: D  139 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8160 (tm-30)
  outliers start: 33
  outliers final: 16
  residues processed: 218
  average time/residue: 0.1034
  time to fit residues: 29.8045
Evaluate side-chains
  199 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 HIS
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  167 PHE
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  276 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 89 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  77 GLN
** D  78 ASN ** 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 = 0.4250 r_free = 0.4250 target = 0.191492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.123942 restraints weight = 11404.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123823 restraints weight = 8042.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.124684 restraints weight = 6123.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.124678 restraints weight = 4783.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.124741 restraints weight = 4533.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8274  Z= 0.149
  Angle     :  1.033  33.928  11217  Z= 0.423
  Chirality :  0.105   2.147   1279
  Planarity :  0.004   0.048   1314
  Dihedral  : 22.687 174.232   1541
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.41 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 26.43 %
    Favored  : 69.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.29), residues: 952
  helix:  1.93 (0.19), residues: 729
  sheet:  None (None), residues: 0
  loop : -2.75 (0.41), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 364 
 TYR   0.014   0.001   TYR D 153 
 PHE   0.018   0.001   PHE C 171 
 TRP   0.022   0.001   TRP D 156 
 HIS   0.008   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 ( 8274)
  covalent geometry    : angle       1.03286 /  0.42 (11217)
  hydrogen bonds       : bond        0.05061 /  3.29 (  547)
  hydrogen bonds       : angle       4.49541 /  3.22 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 196
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.5617 (t70)
REVERT: A  196 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.6843 (ptpp)
REVERT: A  233 GLN cc_start: 0.8123 (mp10) cc_final: 0.7831 (mp10)
REVERT: C  146 LYS cc_start: 0.8052 (tppt) cc_final: 0.7490 (tppt)
REVERT: C  149 GLU cc_start: 0.7972 (pm20) cc_final: 0.7603 (pm20)
REVERT: C  233 GLN cc_start: 0.8010 (mp10) cc_final: 0.7754 (mp10)
REVERT: C  272 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8305 (tp)
REVERT: C  314 LEU cc_start: 0.8789 (mp) cc_final: 0.8441 (mt)
REVERT: B  152 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7589 (ttm-80)
REVERT: D   78 ASN cc_start: 0.8350 (m-40) cc_final: 0.7928 (p0)
REVERT: D  139 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8222 (tm-30)
  outliers start: 34
  outliers final: 21
  residues processed: 214
  average time/residue: 0.0952
  time to fit residues: 27.2481
Evaluate side-chains
  202 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 178
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 HIS
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  196 LYS
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  175 LEU
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  276 THR
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  326 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 51 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 47 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  77 GLN
** D  78 ASN ** 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 = 0.4239 r_free = 0.4239 target = 0.190596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.125446 restraints weight = 11529.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.124684 restraints weight = 7737.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.126062 restraints weight = 6048.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.125964 restraints weight = 4717.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.126182 restraints weight = 4488.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8274  Z= 0.147
  Angle     :  1.019  33.971  11217  Z= 0.417
  Chirality :  0.103   2.102   1279
  Planarity :  0.004   0.067   1314
  Dihedral  : 21.911 178.078   1541
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.41 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 26.31 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.28), residues: 952
  helix:  1.95 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -2.70 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 117 
 TYR   0.017   0.001   TYR C 184 
 PHE   0.016   0.001   PHE A 193 
 TRP   0.026   0.001   TRP D 156 
 HIS   0.009   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 ( 8274)
  covalent geometry    : angle       1.01853 /  0.42 (11217)
  hydrogen bonds       : bond        0.04923 /  3.19 (  547)
  hydrogen bonds       : angle       4.45330 /  3.19 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 190
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 GLN cc_start: 0.8122 (mp10) cc_final: 0.7848 (mp10)
REVERT: C  196 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.6946 (ptpp)
REVERT: C  233 GLN cc_start: 0.8039 (mp10) cc_final: 0.7805 (mp10)
REVERT: C  237 MET cc_start: 0.8146 (tpt) cc_final: 0.7244 (tpt)
REVERT: C  272 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8272 (tp)
REVERT: C  314 LEU cc_start: 0.8802 (mp) cc_final: 0.8480 (mt)
REVERT: B  126 TYR cc_start: 0.5954 (m-10) cc_final: 0.5660 (m-10)
REVERT: B  152 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7631 (ttm-80)
REVERT: D  139 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8058 (tm-30)
  outliers start: 37
  outliers final: 23
  residues processed: 212
  average time/residue: 0.0934
  time to fit residues: 26.9537
Evaluate side-chains
  201 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 HIS
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  196 LYS
Chi-restraints excluded: chain C residue  238 LEU
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  243 ILE
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  319 VAL
Chi-restraints excluded: chain D residue  326 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 79 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 89 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 92 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 34 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 GLN
D  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.187331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.125001 restraints weight = 11476.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.121197 restraints weight = 9273.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.123601 restraints weight = 7937.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.123509 restraints weight = 5632.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.123984 restraints weight = 5226.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8274  Z= 0.195
  Angle     :  1.040  34.295  11217  Z= 0.432
  Chirality :  0.103   2.079   1279
  Planarity :  0.004   0.055   1314
  Dihedral  : 21.316 172.672   1541
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.93 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 26.93 %
    Favored  : 68.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.28), residues: 952
  helix:  1.91 (0.19), residues: 728
  sheet:  None (None), residues: 0
  loop : -2.62 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 324 
 TYR   0.017   0.002   TYR D 140 
 PHE   0.020   0.002   PHE C 171 
 TRP   0.025   0.001   TRP D 156 
 HIS   0.003   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.20 ( 8274)
  covalent geometry    : angle       1.04002 /  0.43 (11217)
  hydrogen bonds       : bond        0.05363 /  3.47 (  547)
  hydrogen bonds       : angle       4.56997 /  3.29 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 178
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.6835 (ptpp)
REVERT: A  233 GLN cc_start: 0.8173 (mp10) cc_final: 0.7874 (mp10)
REVERT: C  146 LYS cc_start: 0.7762 (tppt) cc_final: 0.7061 (tppt)
REVERT: C  149 GLU cc_start: 0.8065 (pm20) cc_final: 0.7653 (pm20)
REVERT: C  233 GLN cc_start: 0.8142 (mp10) cc_final: 0.7864 (mp10)
REVERT: C  272 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8298 (tp)
REVERT: C  314 LEU cc_start: 0.8778 (mp) cc_final: 0.8425 (mt)
REVERT: B  126 TYR cc_start: 0.6002 (m-10) cc_final: 0.5722 (m-10)
REVERT: B  152 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7451 (ttm-80)
  outliers start: 40
  outliers final: 25
  residues processed: 200
  average time/residue: 0.0860
  time to fit residues: 23.5833
Evaluate side-chains
  194 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 167
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 HIS
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  196 LYS
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  141 PHE
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain D residue   90 TRP
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  173 MET
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  243 ILE
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  319 VAL
Chi-restraints excluded: chain D residue  326 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.187662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.124912 restraints weight = 11271.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.123736 restraints weight = 8928.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.124985 restraints weight = 7573.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.125652 restraints weight = 5443.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.125791 restraints weight = 5114.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8274  Z= 0.171
  Angle     :  1.027  34.059  11217  Z= 0.426
  Chirality :  0.102   2.077   1279
  Planarity :  0.004   0.047   1314
  Dihedral  : 21.039 173.525   1541
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.14 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 27.93 %
    Favored  : 67.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.29), residues: 952
  helix:  1.95 (0.19), residues: 732
  sheet:  None (None), residues: 0
  loop : -2.66 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 324 
 TYR   0.017   0.001   TYR C 184 
 PHE   0.018   0.001   PHE A 193 
 TRP   0.029   0.001   TRP D 156 
 HIS   0.003   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.17 ( 8274)
  covalent geometry    : angle       1.02742 /  0.43 (11217)
  hydrogen bonds       : bond        0.05183 /  3.35 (  547)
  hydrogen bonds       : angle       4.53165 /  3.26 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 175
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 PHE cc_start: 0.6993 (m-80) cc_final: 0.6587 (m-80)
REVERT: A  196 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6822 (ptpp)
REVERT: A  233 GLN cc_start: 0.8155 (mp10) cc_final: 0.7868 (mp10)
REVERT: C  233 GLN cc_start: 0.8135 (mp10) cc_final: 0.7883 (mp10)
REVERT: C  272 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8357 (tp)
REVERT: C  296 MET cc_start: 0.6228 (mmm) cc_final: 0.4762 (mpp)
REVERT: C  314 LEU cc_start: 0.8800 (mp) cc_final: 0.8447 (mt)
REVERT: B  126 TYR cc_start: 0.5960 (m-10) cc_final: 0.5698 (m-10)
REVERT: B  152 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7309 (ttt180)
REVERT: D   78 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7647 (p0)
  outliers start: 37
  outliers final: 26
  residues processed: 197
  average time/residue: 0.0922
  time to fit residues: 24.2879
Evaluate side-chains
  193 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 164
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 HIS
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  196 LYS
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  196 LYS
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   90 TRP
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  243 ILE
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  326 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 92 optimal weight:    0.4980
   chunk 30 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    0.8586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.189194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.126526 restraints weight = 11353.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.124121 restraints weight = 9134.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.125518 restraints weight = 7983.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.126507 restraints weight = 5654.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.126906 restraints weight = 5048.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8274  Z= 0.152
  Angle     :  1.031  33.790  11217  Z= 0.430
  Chirality :  0.102   2.080   1279
  Planarity :  0.004   0.047   1314
  Dihedral  : 20.735 174.171   1541
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.14 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 29.18 %
    Favored  : 66.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.29), residues: 952
  helix:  1.98 (0.19), residues: 734
  sheet:  None (None), residues: 0
  loop : -2.60 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 364 
 TYR   0.018   0.001   TYR D 153 
 PHE   0.029   0.001   PHE C 171 
 TRP   0.030   0.001   TRP D 156 
 HIS   0.002   0.000   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.15 ( 8274)
  covalent geometry    : angle       1.03143 /  0.43 (11217)
  hydrogen bonds       : bond        0.04947 /  3.20 (  547)
  hydrogen bonds       : angle       4.50978 /  3.23 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 176
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 PHE cc_start: 0.7078 (m-80) cc_final: 0.6733 (m-80)
REVERT: A  196 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.6922 (ptpp)
REVERT: A  233 GLN cc_start: 0.8132 (mp10) cc_final: 0.7839 (mp10)
REVERT: C  196 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.6828 (ptpp)
REVERT: C  233 GLN cc_start: 0.8126 (mp10) cc_final: 0.7896 (mp10)
REVERT: C  296 MET cc_start: 0.6158 (mmm) cc_final: 0.4721 (mpp)
REVERT: C  314 LEU cc_start: 0.8746 (mp) cc_final: 0.8402 (mt)
REVERT: B  126 TYR cc_start: 0.5900 (m-10) cc_final: 0.5678 (m-10)
REVERT: B  152 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.6970 (ttt180)
REVERT: D   78 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7717 (p0)
  outliers start: 35
  outliers final: 29
  residues processed: 196
  average time/residue: 0.0906
  time to fit residues: 24.3303
Evaluate side-chains
  199 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 167
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 HIS
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  196 LYS
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  196 LYS
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   90 TRP
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  243 ILE
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  319 VAL
Chi-restraints excluded: chain D residue  326 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 19 optimal weight:    0.3980
   chunk 63 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.188288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.128684 restraints weight = 11261.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.127631 restraints weight = 9778.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.128940 restraints weight = 9607.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.128876 restraints weight = 6175.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.129823 restraints weight = 5585.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   8274  Z= 0.169
  Angle     :  1.036  33.859  11217  Z= 0.433
  Chirality :  0.102   2.075   1279
  Planarity :  0.004   0.046   1314
  Dihedral  : 20.494 174.348   1541
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.04 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 28.55 %
    Favored  : 66.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.29), residues: 952
  helix:  1.95 (0.19), residues: 734
  sheet:  None (None), residues: 0
  loop : -2.62 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 324 
 TYR   0.021   0.001   TYR B 140 
 PHE   0.030   0.001   PHE C 171 
 TRP   0.034   0.001   TRP D 156 
 HIS   0.003   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.17 ( 8274)
  covalent geometry    : angle       1.03647 /  0.43 (11217)
  hydrogen bonds       : bond        0.05089 /  3.29 (  547)
  hydrogen bonds       : angle       4.50316 /  3.23 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 175
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 PHE cc_start: 0.6988 (m-80) cc_final: 0.6734 (m-80)
REVERT: A  196 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7079 (ptpp)
REVERT: A  233 GLN cc_start: 0.8136 (mp10) cc_final: 0.7847 (mp10)
REVERT: C  196 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.6863 (ptpp)
REVERT: C  233 GLN cc_start: 0.8144 (mp10) cc_final: 0.7908 (mp10)
REVERT: C  296 MET cc_start: 0.6070 (mmm) cc_final: 0.4694 (mpp)
REVERT: C  314 LEU cc_start: 0.8798 (mp) cc_final: 0.8455 (mt)
REVERT: B  126 TYR cc_start: 0.5903 (m-10) cc_final: 0.5667 (m-10)
REVERT: D   78 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7665 (p0)
  outliers start: 39
  outliers final: 28
  residues processed: 197
  average time/residue: 0.0884
  time to fit residues: 23.7550
Evaluate side-chains
  200 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 169
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 HIS
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  196 LYS
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  196 LYS
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  167 PHE
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   90 TRP
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  243 ILE
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  319 VAL
Chi-restraints excluded: chain D residue  326 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    1.9388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.186049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.127523 restraints weight = 11223.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128334 restraints weight = 10703.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.129055 restraints weight = 8583.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.129895 restraints weight = 5754.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.130212 restraints weight = 4985.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   8274  Z= 0.214
  Angle     :  1.057  34.140  11217  Z= 0.447
  Chirality :  0.102   2.061   1279
  Planarity :  0.005   0.099   1314
  Dihedral  : 20.393 174.116   1541
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.93 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 29.18 %
    Favored  : 66.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.29), residues: 952
  helix:  1.84 (0.19), residues: 734
  sheet:  None (None), residues: 0
  loop : -2.64 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 324 
 TYR   0.025   0.002   TYR B 140 
 PHE   0.046   0.002   PHE B 162 
 TRP   0.037   0.001   TRP D 156 
 HIS   0.004   0.001   HIS C 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00493 /  0.21 ( 8274)
  covalent geometry    : angle       1.05707 /  0.45 (11217)
  hydrogen bonds       : bond        0.05473 /  3.54 (  547)
  hydrogen bonds       : angle       4.64454 /  3.33 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 173
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7065 (ptpp)
REVERT: A  233 GLN cc_start: 0.8179 (mp10) cc_final: 0.7872 (mp10)
REVERT: C  130 PHE cc_start: 0.6977 (m-10) cc_final: 0.6711 (m-80)
REVERT: C  196 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7055 (ptpp)
REVERT: C  233 GLN cc_start: 0.8202 (mp10) cc_final: 0.7917 (mp10)
REVERT: C  272 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8262 (tp)
REVERT: C  296 MET cc_start: 0.6110 (mmm) cc_final: 0.4729 (mpp)
REVERT: C  314 LEU cc_start: 0.8555 (mp) cc_final: 0.8190 (mt)
REVERT: B  126 TYR cc_start: 0.5912 (m-10) cc_final: 0.5696 (m-10)
REVERT: D   78 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7407 (p0)
  outliers start: 36
  outliers final: 28
  residues processed: 193
  average time/residue: 0.0924
  time to fit residues: 24.2449
Evaluate side-chains
  197 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 165
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  196 LYS
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  196 LYS
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  167 PHE
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   90 TRP
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  243 ILE
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  319 VAL
Chi-restraints excluded: chain D residue  326 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 68 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.188715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.129863 restraints weight = 11288.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.124647 restraints weight = 10122.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.125885 restraints weight = 9336.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.127924 restraints weight = 6327.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.127929 restraints weight = 5058.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8274  Z= 0.156
  Angle     :  1.048  33.576  11217  Z= 0.441
  Chirality :  0.102   2.071   1279
  Planarity :  0.005   0.080   1314
  Dihedral  : 20.160 174.494   1539
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.62 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 30.17 %
    Favored  : 66.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.29), residues: 952
  helix:  1.92 (0.19), residues: 734
  sheet:  None (None), residues: 0
  loop : -2.66 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 324 
 TYR   0.054   0.001   TYR D 140 
 PHE   0.047   0.002   PHE B 162 
 TRP   0.039   0.001   TRP D 156 
 HIS   0.010   0.001   HIS A 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.16 ( 8274)
  covalent geometry    : angle       1.04828 /  0.44 (11217)
  hydrogen bonds       : bond        0.05026 /  3.24 (  547)
  hydrogen bonds       : angle       4.54614 /  3.25 ( 1641)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7162 (ptpp)
REVERT: A  233 GLN cc_start: 0.8139 (mp10) cc_final: 0.7854 (mp10)
REVERT: C  130 PHE cc_start: 0.6984 (m-10) cc_final: 0.6700 (m-80)
REVERT: C  196 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7150 (ptpp)
REVERT: C  233 GLN cc_start: 0.8154 (mp10) cc_final: 0.7887 (mp10)
REVERT: C  296 MET cc_start: 0.6112 (mmm) cc_final: 0.4686 (mpp)
REVERT: C  314 LEU cc_start: 0.8731 (mp) cc_final: 0.8369 (mt)
REVERT: B  126 TYR cc_start: 0.5974 (m-10) cc_final: 0.5738 (m-10)
REVERT: D   78 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7519 (p0)
REVERT: D  139 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: D  161 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8897 (pttp)
  outliers start: 28
  outliers final: 23
  residues processed: 189
  average time/residue: 0.0905
  time to fit residues: 23.3676
Evaluate side-chains
  195 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 169
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  196 LYS
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  196 LYS
Chi-restraints excluded: chain C residue  272 LEU
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue  167 PHE
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   90 TRP
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  204 ILE
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  243 ILE
Chi-restraints excluded: chain D residue  272 ILE
Chi-restraints excluded: chain D residue  297 THR
Chi-restraints excluded: chain D residue  319 VAL
Chi-restraints excluded: chain D residue  326 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 68 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 78 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.189409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.128549 restraints weight = 11319.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.124787 restraints weight = 9204.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.125817 restraints weight = 8960.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.127497 restraints weight = 6533.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.127642 restraints weight = 5541.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   8274  Z= 0.157
  Angle     :  1.065  33.491  11217  Z= 0.446
  Chirality :  0.102   2.059   1279
  Planarity :  0.004   0.072   1314
  Dihedral  : 20.033 174.826   1539
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.51 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 30.67 %
    Favored  : 66.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.29), residues: 952
  helix:  1.96 (0.19), residues: 734
  sheet:  None (None), residues: 0
  loop : -2.65 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 364 
 TYR   0.021   0.001   TYR D 153 
 PHE   0.038   0.001   PHE B 162 
 TRP   0.037   0.001   TRP D 156 
 HIS   0.007   0.001   HIS A 126 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.16 ( 8274)
  covalent geometry    : angle       1.06514 /  0.45 (11217)
  hydrogen bonds       : bond        0.04938 /  3.19 (  547)
  hydrogen bonds       : angle       4.51171 /  3.22 ( 1641)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1541.73 seconds
wall clock time: 27 minutes 19.37 seconds (1639.37 seconds total)