Starting phenix.real_space_refine
on Sun Apr  5 06:42:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jv5_22493/04_2026/7jv5_22493.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jv5_22493/04_2026/7jv5_22493.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jv5_22493/04_2026/7jv5_22493.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jv5_22493/04_2026/7jv5_22493.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jv5_22493/04_2026/7jv5_22493.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jv5_22493/04_2026/7jv5_22493.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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
     S      54      5.16       5
     Cl      1      4.86       5
     C    5493      2.51       5
     N    1444      2.21       5
     O    1539      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8531
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2244
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 10, 'TRANS': 271}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1978
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1978
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2604
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 296
          Unusual residues: {'CLR': 6, 'PLM': 6, 'SK0': 1}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
  Time building chain proxies: 2.09, per 1000 atoms: 0.24
  Number of scatterers: 8531
  At special positions: 0
  Unit cell: (106.47, 98.358, 120.666, 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)
     Cl      1     17.00
     S      54     16.00
     O    1539      8.00
     N    1444      7.00
     C    5493      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  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: 0.70
  Conformation dependent library (CDL) restraints added in 288.6 milliseconds
  

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1976

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      44.1% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'R' and resid 21 through 51
    Processing helix  chain 'R' and resid 52 through 57
      removed outlier: 3.826A  pdb=" N   LYS R  57 " --> pdb=" O   HIS R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 77
      removed outlier: 4.148A  pdb=" N   VAL R  63 " --> pdb=" O   THR R  59 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 88
    Processing helix  chain 'R' and resid 94 through 127
      removed outlier: 4.477A  pdb=" N   ILE R  98 " --> pdb=" O   SER R  94 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 135
    Processing helix  chain 'R' and resid 136 through 156
    Processing helix  chain 'R' and resid 157 through 162
    Processing helix  chain 'R' and resid 191 through 203
    Processing helix  chain 'R' and resid 203 through 240
    Processing helix  chain 'R' and resid 264 through 295
      removed outlier: 3.998A  pdb=" N   PHE R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
    Processing helix  chain 'R' and resid 296 through 298
      No H-bonds generated for 'chain 'R' and resid 296 through 298'
    Processing helix  chain 'R' and resid 309 through 332
      removed outlier: 4.580A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   SER R 325 " --> pdb=" O   TRP R 321 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU R 326 " --> pdb=" O   ALA R 322 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 346
    Processing helix  chain 'A' and resid 10 through 40
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 234 through 240
      removed outlier: 3.595A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 4.055A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 4.219A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 312
      removed outlier: 3.948A  pdb=" N   ASP A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.554A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 4.191A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.736A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 61 through 65
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.979A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.600A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.599A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.157A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.904A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.773A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.681A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.780A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.590A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1308 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: 1.23

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2419
        1.34 -     1.46: 1815
        1.46 -     1.58: 4404
        1.58 -     1.70: 0
        1.70 -     1.83: 74
  Bond restraints: 8712
  Sorted by residual:
  bond pdb=" C   MET R  78 "
       pdb=" N   PRO R  79 "
    ideal  model  delta    sigma   weight residual
    1.334  1.385 -0.051 2.34e-02 1.83e+03 4.76e+00
  bond pdb=" C   ILE R 157 "
       pdb=" N   PRO R 158 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.20e-02 6.94e+03 3.59e+00
  bond pdb=" CA  PHE R 297 "
       pdb=" C   PHE R 297 "
    ideal  model  delta    sigma   weight residual
    1.523  1.557 -0.033 1.80e-02 3.09e+03 3.42e+00
  bond pdb=" C   LEU R 295 "
       pdb=" N   PRO R 296 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.025 1.36e-02 5.41e+03 3.35e+00
  bond pdb=" C   ASN R 327 "
       pdb=" N   PRO R 328 "
    ideal  model  delta    sigma   weight residual
    1.334  1.376 -0.042 2.34e-02 1.83e+03 3.27e+00
  ... (remaining 8707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 10959
        2.05 -     4.09: 742
        4.09 -     6.14: 71
        6.14 -     8.18: 19
        8.18 -    10.23: 5
  Bond angle restraints: 11796
  Sorted by residual:
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     122.08  128.51   -6.43 1.47e+00 4.63e-01 1.91e+01
  angle pdb=" N   MET R  78 "
        pdb=" CA  MET R  78 "
        pdb=" C   MET R  78 "
      ideal   model   delta    sigma   weight residual
     109.81  119.30   -9.49 2.21e+00 2.05e-01 1.84e+01
  angle pdb=" N   GLU A  16 "
        pdb=" CA  GLU A  16 "
        pdb=" C   GLU A  16 "
      ideal   model   delta    sigma   weight residual
     111.11  116.04   -4.93 1.20e+00 6.94e-01 1.69e+01
  angle pdb=" N   ILE B  33 "
        pdb=" CA  ILE B  33 "
        pdb=" C   ILE B  33 "
      ideal   model   delta    sigma   weight residual
     110.62  115.17   -4.55 1.14e+00 7.69e-01 1.59e+01
  angle pdb=" N   LYS A  17 "
        pdb=" CA  LYS A  17 "
        pdb=" C   LYS A  17 "
      ideal   model   delta    sigma   weight residual
     111.37  117.33   -5.96 1.65e+00 3.67e-01 1.31e+01
  ... (remaining 11791 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.04: 5177
       15.04 -    30.07: 282
       30.07 -    45.11: 46
       45.11 -    60.15: 4
       60.15 -    75.18: 2
  Dihedral angle restraints: 5511
    sinusoidal: 2469
      harmonic: 3042
  Sorted by residual:
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.14   26.86     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  SER N  49 "
           pdb=" C   SER N  49 "
           pdb=" N   ASP N  50 "
           pdb=" CA  ASP N  50 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.23  -26.77     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  LEU B 198 "
           pdb=" C   LEU B 198 "
           pdb=" N   PHE B 199 "
           pdb=" CA  PHE B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.33   25.67     0      5.00e+00 4.00e-02 2.64e+01
  ... (remaining 5508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1127
       0.085 -    0.170: 169
       0.170 -    0.254: 24
       0.254 -    0.339: 7
       0.339 -    0.424: 7
  Chirality restraints: 1334
  Sorted by residual:
  chirality pdb=" C14 CLR R 502 "
            pdb=" C13 CLR R 502 "
            pdb=" C15 CLR R 502 "
            pdb=" C8  CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.74    0.42 2.00e-01 2.50e+01 4.49e+00
  chirality pdb=" C14 CLR R 507 "
            pdb=" C13 CLR R 507 "
            pdb=" C15 CLR R 507 "
            pdb=" C8  CLR R 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.74    0.42 2.00e-01 2.50e+01 4.45e+00
  chirality pdb=" C14 CLR R 504 "
            pdb=" C13 CLR R 504 "
            pdb=" C15 CLR R 504 "
            pdb=" C8  CLR R 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.72    0.40 2.00e-01 2.50e+01 3.96e+00
  ... (remaining 1331 not shown)

  Planarity restraints: 1453
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 207 "    0.022 2.00e-02 2.50e+03   4.26e-02 1.82e+01
        pdb=" C   VAL R 207 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   VAL R 207 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ALA R 208 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 218 "   -0.021 2.00e-02 2.50e+03   4.21e-02 1.77e+01
        pdb=" C   TYR R 218 "    0.073 2.00e-02 2.50e+03
        pdb=" O   TYR R 218 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ARG R 219 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 272 "    0.021 2.00e-02 2.50e+03   4.19e-02 1.75e+01
        pdb=" C   LYS R 272 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   LYS R 272 "    0.027 2.00e-02 2.50e+03
        pdb=" N   THR R 273 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1450 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1224
        2.77 -     3.30: 7752
        3.30 -     3.84: 13286
        3.84 -     4.37: 15683
        4.37 -     4.90: 27429
  Nonbonded interactions: 65374
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   TRP N  47 "
            pdb=" OG1 THR N  61 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" NE2 GLN B  75 "
            pdb=" O   VAL B 100 "
     model   vdw
     2.345 3.120
  ... (remaining 65369 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.790
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
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   0.051   8716  Z= 0.263
  Angle     :  1.087  10.230  11804  Z= 0.624
  Chirality :  0.070   0.424   1334
  Planarity :  0.009   0.076   1453
  Dihedral  :  9.419  75.182   3523
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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: -3.02 (0.22), residues: 1024
  helix: -2.90 (0.18), residues: 413
  sheet: -0.01 (0.33), residues: 232
  loop : -2.01 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 385 
 TYR   0.020   0.002   TYR R 331 
 PHE   0.040   0.003   PHE B 234 
 TRP   0.023   0.003   TRP N  36 
 HIS   0.010   0.003   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 8712)
  covalent geometry    : angle       1.08720 (11796)
  SS BOND              : bond        0.00304 (    4)
  SS BOND              : angle       1.23926 (    8)
  hydrogen bonds       : bond        0.13551 (  452)
  hydrogen bonds       : angle       7.02221 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  307 LYS cc_start: 0.7224 (mmmt) cc_final: 0.5561 (tttm)
REVERT: A  317 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8225 (ptt-90)
REVERT: A  392 GLU cc_start: 0.8387 (tt0) cc_final: 0.7943 (tp30)
REVERT: B   46 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7486 (mtp-110)
REVERT: B  134 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.6768 (pmt170)
REVERT: B  163 ASP cc_start: 0.8713 (p0) cc_final: 0.8502 (p0)
REVERT: B  175 GLN cc_start: 0.8563 (mt0) cc_final: 0.7951 (mm-40)
REVERT: B  217 MET cc_start: 0.8622 (ptt) cc_final: 0.8300 (ppp)
REVERT: B  226 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8540 (mt-10)
REVERT: B  239 ASN cc_start: 0.8036 (m-40) cc_final: 0.7240 (t0)
REVERT: B  303 ASP cc_start: 0.7805 (t0) cc_final: 0.7472 (p0)
REVERT: B  315 VAL cc_start: 0.8675 (t) cc_final: 0.8259 (p)
REVERT: G   21 MET cc_start: 0.8095 (mtt) cc_final: 0.7405 (tmm)
REVERT: G   61 PHE cc_start: 0.8183 (m-80) cc_final: 0.7903 (m-80)
REVERT: N   53 GLN cc_start: 0.8493 (mp10) cc_final: 0.8293 (mp10)
REVERT: N   72 ARG cc_start: 0.8322 (ptm160) cc_final: 0.8062 (ppp80)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.6531
  time to fit residues: 129.4535
Evaluate side-chains
  106 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 220 HIS
A 262 GLN
A 371 ASN
A 387 HIS
B 142 HIS
B 176 GLN
B 266 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.181441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.134445 restraints weight = 9492.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 3.22
r_work: 0.3693 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6351
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8716  Z= 0.171
  Angle     :  0.606   6.688  11804  Z= 0.320
  Chirality :  0.043   0.170   1334
  Planarity :  0.005   0.047   1453
  Dihedral  :  6.725  58.008   1625
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 10.26 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.24), residues: 1024
  helix:  0.43 (0.23), residues: 422
  sheet:  0.38 (0.34), residues: 226
  loop : -1.34 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  27 
 TYR   0.014   0.002   TYR B 105 
 PHE   0.016   0.002   PHE R 333 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.005   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8712)
  covalent geometry    : angle       0.60535 (11796)
  SS BOND              : bond        0.00253 (    4)
  SS BOND              : angle       1.00699 (    8)
  hydrogen bonds       : bond        0.05161 (  452)
  hydrogen bonds       : angle       5.00817 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  227 ARG cc_start: 0.6940 (mtm-85) cc_final: 0.6577 (mtp180)
REVERT: A  221 MET cc_start: 0.7925 (ttm) cc_final: 0.7674 (ttt)
REVERT: A  229 ASP cc_start: 0.7929 (t0) cc_final: 0.7392 (p0)
REVERT: A  307 LYS cc_start: 0.6762 (mmmt) cc_final: 0.5444 (tttm)
REVERT: A  314 GLU cc_start: 0.7755 (mt-10) cc_final: 0.6891 (pm20)
REVERT: A  317 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7891 (ptt-90)
REVERT: A  343 ASP cc_start: 0.7858 (m-30) cc_final: 0.7641 (m-30)
REVERT: A  392 GLU cc_start: 0.7902 (tt0) cc_final: 0.7332 (tp30)
REVERT: B   46 ARG cc_start: 0.6863 (ttm-80) cc_final: 0.6318 (mtp85)
REVERT: B   68 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7163 (mmm-85)
REVERT: B   75 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7095 (mp10)
REVERT: B  134 ARG cc_start: 0.6475 (mtm-85) cc_final: 0.5942 (pmt170)
REVERT: B  175 GLN cc_start: 0.7738 (mt0) cc_final: 0.7019 (mm-40)
REVERT: B  189 SER cc_start: 0.8439 (p) cc_final: 0.8222 (m)
REVERT: B  205 ASP cc_start: 0.6968 (p0) cc_final: 0.6588 (p0)
REVERT: B  212 ASP cc_start: 0.6875 (t0) cc_final: 0.6486 (t0)
REVERT: B  214 ARG cc_start: 0.8736 (tpp80) cc_final: 0.8439 (tpp80)
REVERT: B  217 MET cc_start: 0.7841 (ptt) cc_final: 0.7304 (ppp)
REVERT: B  226 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7735 (mt-10)
REVERT: B  239 ASN cc_start: 0.7215 (m-40) cc_final: 0.6691 (t0)
REVERT: B  254 ASP cc_start: 0.7716 (t0) cc_final: 0.7422 (t0)
REVERT: B  277 SER cc_start: 0.9061 (t) cc_final: 0.8839 (p)
REVERT: B  298 ASP cc_start: 0.7522 (t0) cc_final: 0.7091 (t70)
REVERT: B  303 ASP cc_start: 0.6821 (t0) cc_final: 0.6384 (p0)
REVERT: B  315 VAL cc_start: 0.8540 (t) cc_final: 0.8295 (p)
REVERT: G   21 MET cc_start: 0.7558 (mtt) cc_final: 0.6959 (tmm)
REVERT: N   53 GLN cc_start: 0.7776 (mp10) cc_final: 0.7483 (mp10)
REVERT: N  123 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7244 (tm-30)
  outliers start: 26
  outliers final: 11
  residues processed: 149
  average time/residue: 0.6117
  time to fit residues: 96.6391
Evaluate side-chains
  127 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  152 VAL
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 83 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    0.4980
   chunk 52 optimal weight:    9.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 262 GLN
A 390 GLN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.182281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.134947 restraints weight = 9343.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 3.25
r_work: 0.3670 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6306
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061   8716  Z= 0.113
  Angle     :  0.513   6.391  11804  Z= 0.267
  Chirality :  0.041   0.160   1334
  Planarity :  0.004   0.044   1453
  Dihedral  :  6.354  59.511   1625
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.82 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.26), residues: 1024
  helix:  2.00 (0.24), residues: 428
  sheet:  0.43 (0.34), residues: 224
  loop : -1.16 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.009   0.001   TYR N 117 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 8712)
  covalent geometry    : angle       0.51231 (11796)
  SS BOND              : bond        0.00157 (    4)
  SS BOND              : angle       0.83122 (    8)
  hydrogen bonds       : bond        0.04478 (  452)
  hydrogen bonds       : angle       4.57509 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   60 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6725 (mpt)
REVERT: A  221 MET cc_start: 0.7789 (ttm) cc_final: 0.7501 (ttp)
REVERT: A  229 ASP cc_start: 0.7951 (t0) cc_final: 0.7697 (t70)
REVERT: A  314 GLU cc_start: 0.7819 (mt-10) cc_final: 0.6937 (pm20)
REVERT: A  317 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7920 (ptt-90)
REVERT: A  392 GLU cc_start: 0.7960 (tt0) cc_final: 0.7403 (tp30)
REVERT: B   68 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7098 (mmm-85)
REVERT: B  134 ARG cc_start: 0.6458 (mtm-85) cc_final: 0.5813 (pmt170)
REVERT: B  138 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8114 (mm-30)
REVERT: B  175 GLN cc_start: 0.7605 (mt0) cc_final: 0.6995 (mm-40)
REVERT: B  189 SER cc_start: 0.8428 (p) cc_final: 0.8164 (m)
REVERT: B  205 ASP cc_start: 0.7075 (p0) cc_final: 0.6686 (p0)
REVERT: B  212 ASP cc_start: 0.6784 (t0) cc_final: 0.6476 (t0)
REVERT: B  217 MET cc_start: 0.7878 (ptt) cc_final: 0.7405 (ppp)
REVERT: B  226 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7814 (mt-10)
REVERT: B  239 ASN cc_start: 0.7021 (m-40) cc_final: 0.6214 (t0)
REVERT: B  254 ASP cc_start: 0.7679 (t0) cc_final: 0.7414 (t0)
REVERT: B  277 SER cc_start: 0.9113 (t) cc_final: 0.8899 (p)
REVERT: B  298 ASP cc_start: 0.7340 (t0) cc_final: 0.6818 (t0)
REVERT: B  303 ASP cc_start: 0.6616 (t0) cc_final: 0.6203 (p0)
REVERT: B  315 VAL cc_start: 0.8508 (t) cc_final: 0.8289 (p)
REVERT: B  339 TRP cc_start: 0.8597 (m100) cc_final: 0.8076 (m-10)
REVERT: G   21 MET cc_start: 0.7432 (mtt) cc_final: 0.6901 (tmm)
REVERT: N   53 GLN cc_start: 0.7838 (mp10) cc_final: 0.7449 (mp10)
REVERT: N  105 ARG cc_start: 0.7414 (mpp-170) cc_final: 0.6825 (mtm180)
  outliers start: 24
  outliers final: 10
  residues processed: 133
  average time/residue: 0.5992
  time to fit residues: 84.5986
Evaluate side-chains
  112 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 99 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.180590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.132809 restraints weight = 9505.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 3.27
r_work: 0.3647 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6331
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8716  Z= 0.117
  Angle     :  0.506   6.418  11804  Z= 0.262
  Chirality :  0.041   0.192   1334
  Planarity :  0.004   0.046   1453
  Dihedral  :  6.224  58.013   1625
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 13.38 %
    Favored  : 83.84 %
  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:  1.15 (0.26), residues: 1024
  helix:  2.39 (0.25), residues: 434
  sheet:  0.40 (0.34), residues: 229
  loop : -1.05 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.008   0.001   TYR R 194 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8712)
  covalent geometry    : angle       0.50582 (11796)
  SS BOND              : bond        0.00110 (    4)
  SS BOND              : angle       0.81609 (    8)
  hydrogen bonds       : bond        0.04332 (  452)
  hydrogen bonds       : angle       4.43344 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.312 
Fit side-chains
REVERT: R  132 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7573 (mt-10)
REVERT: A  314 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7367 (mt-10)
REVERT: A  317 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.8028 (ptt90)
REVERT: A  392 GLU cc_start: 0.7989 (tt0) cc_final: 0.7340 (tp30)
REVERT: B   68 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7116 (mmm-85)
REVERT: B  134 ARG cc_start: 0.6604 (mtm-85) cc_final: 0.5821 (pmt170)
REVERT: B  175 GLN cc_start: 0.7834 (mt0) cc_final: 0.7137 (mm110)
REVERT: B  180 PHE cc_start: 0.4234 (OUTLIER) cc_final: 0.1888 (p90)
REVERT: B  189 SER cc_start: 0.8411 (p) cc_final: 0.8163 (m)
REVERT: B  205 ASP cc_start: 0.7091 (p0) cc_final: 0.6718 (p0)
REVERT: B  212 ASP cc_start: 0.6753 (t0) cc_final: 0.6501 (t0)
REVERT: B  214 ARG cc_start: 0.8886 (tpp80) cc_final: 0.8545 (tpp80)
REVERT: B  217 MET cc_start: 0.7815 (ptt) cc_final: 0.7410 (ppp)
REVERT: B  226 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7860 (mt-10)
REVERT: B  239 ASN cc_start: 0.7183 (m-40) cc_final: 0.6772 (t0)
REVERT: B  254 ASP cc_start: 0.7716 (t0) cc_final: 0.7473 (t0)
REVERT: B  303 ASP cc_start: 0.6622 (t0) cc_final: 0.6186 (p0)
REVERT: B  339 TRP cc_start: 0.8584 (m100) cc_final: 0.7990 (m-10)
REVERT: G   21 MET cc_start: 0.7314 (mtt) cc_final: 0.6809 (tmm)
REVERT: N   53 GLN cc_start: 0.7798 (mp10) cc_final: 0.7334 (mp10)
REVERT: N  105 ARG cc_start: 0.7407 (mpp-170) cc_final: 0.6818 (mtm180)
  outliers start: 25
  outliers final: 11
  residues processed: 116
  average time/residue: 0.6526
  time to fit residues: 80.2023
Evaluate side-chains
  105 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 85 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 67 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.9384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.179982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.133041 restraints weight = 9580.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 3.20
r_work: 0.3676 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6224
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8716  Z= 0.119
  Angle     :  0.511   7.624  11804  Z= 0.264
  Chirality :  0.041   0.152   1334
  Planarity :  0.004   0.048   1453
  Dihedral  :  6.142  57.772   1625
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.16 %
    Favored  : 83.39 %
  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:  1.22 (0.27), residues: 1024
  helix:  2.57 (0.25), residues: 435
  sheet:  0.21 (0.33), residues: 232
  loop : -1.05 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  27 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8712)
  covalent geometry    : angle       0.51089 (11796)
  SS BOND              : bond        0.00085 (    4)
  SS BOND              : angle       0.81026 (    8)
  hydrogen bonds       : bond        0.04286 (  452)
  hydrogen bonds       : angle       4.36876 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: R  132 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7522 (mt-10)
REVERT: A   60 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6621 (mpt)
REVERT: A  221 MET cc_start: 0.7021 (ttp) cc_final: 0.6645 (tpt)
REVERT: A  314 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7163 (pm20)
REVERT: A  317 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.8002 (ptt-90)
REVERT: A  392 GLU cc_start: 0.7957 (tt0) cc_final: 0.7239 (tp30)
REVERT: B   68 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.7007 (mmm-85)
REVERT: B  134 ARG cc_start: 0.6594 (mtm-85) cc_final: 0.5711 (pmt170)
REVERT: B  161 SER cc_start: 0.8860 (t) cc_final: 0.8540 (p)
REVERT: B  175 GLN cc_start: 0.7730 (mt0) cc_final: 0.7056 (mm110)
REVERT: B  180 PHE cc_start: 0.4390 (OUTLIER) cc_final: 0.1805 (p90)
REVERT: B  189 SER cc_start: 0.8367 (p) cc_final: 0.8088 (m)
REVERT: B  205 ASP cc_start: 0.6995 (p0) cc_final: 0.6653 (p0)
REVERT: B  212 ASP cc_start: 0.6617 (t0) cc_final: 0.6356 (t0)
REVERT: B  214 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8604 (tpp80)
REVERT: B  217 MET cc_start: 0.7783 (ptt) cc_final: 0.7292 (ppp)
REVERT: B  239 ASN cc_start: 0.7129 (m-40) cc_final: 0.6722 (t0)
REVERT: B  254 ASP cc_start: 0.7724 (t0) cc_final: 0.7482 (t0)
REVERT: B  298 ASP cc_start: 0.7771 (t70) cc_final: 0.7449 (t70)
REVERT: B  303 ASP cc_start: 0.6577 (t0) cc_final: 0.6135 (p0)
REVERT: B  339 TRP cc_start: 0.8531 (m100) cc_final: 0.7898 (m-10)
REVERT: G   21 MET cc_start: 0.6979 (mtt) cc_final: 0.6524 (tmm)
REVERT: G   27 ARG cc_start: 0.7667 (mtt90) cc_final: 0.7438 (mtt90)
REVERT: N   98 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8174 (ttp80)
REVERT: N  105 ARG cc_start: 0.7355 (mpp-170) cc_final: 0.6759 (mtm180)
REVERT: N  123 GLN cc_start: 0.7045 (tm-30) cc_final: 0.6780 (tm-30)
  outliers start: 22
  outliers final: 11
  residues processed: 110
  average time/residue: 0.6512
  time to fit residues: 75.9128
Evaluate side-chains
  107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  132 GLU
Chi-restraints excluded: chain R residue  283 CYS
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   68 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   78 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    0.0980
   chunk 90 optimal weight:   20.0000
   chunk 75 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
R  41 ASN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.174407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.127515 restraints weight = 9650.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 3.14
r_work: 0.3597 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6293
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8716  Z= 0.173
  Angle     :  0.570   7.343  11804  Z= 0.293
  Chirality :  0.043   0.153   1334
  Planarity :  0.004   0.047   1453
  Dihedral  :  6.576  57.712   1625
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 13.27 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.27), residues: 1024
  helix:  2.51 (0.25), residues: 428
  sheet: -0.12 (0.32), residues: 239
  loop : -0.99 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  27 
 TYR   0.014   0.001   TYR A 339 
 PHE   0.014   0.002   PHE B 199 
 TRP   0.011   0.001   TRP R  80 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8712)
  covalent geometry    : angle       0.56968 (11796)
  SS BOND              : bond        0.00172 (    4)
  SS BOND              : angle       0.95619 (    8)
  hydrogen bonds       : bond        0.04888 (  452)
  hydrogen bonds       : angle       4.50623 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  132 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7584 (mt-10)
REVERT: A   60 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6422 (mpt)
REVERT: A  229 ASP cc_start: 0.8035 (t0) cc_final: 0.7545 (t0)
REVERT: A  314 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7241 (pm20)
REVERT: A  317 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8002 (ptt-90)
REVERT: A  392 GLU cc_start: 0.8034 (tt0) cc_final: 0.7292 (tp30)
REVERT: B   75 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7866 (mm110)
REVERT: B  134 ARG cc_start: 0.6454 (mtm-85) cc_final: 0.5518 (pmt170)
REVERT: B  138 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8311 (tp30)
REVERT: B  161 SER cc_start: 0.9104 (t) cc_final: 0.8665 (p)
REVERT: B  175 GLN cc_start: 0.7658 (mt0) cc_final: 0.7149 (mp10)
REVERT: B  180 PHE cc_start: 0.4852 (OUTLIER) cc_final: 0.2655 (p90)
REVERT: B  189 SER cc_start: 0.8421 (p) cc_final: 0.8193 (m)
REVERT: B  205 ASP cc_start: 0.7107 (p0) cc_final: 0.6800 (p0)
REVERT: B  214 ARG cc_start: 0.8872 (tpp80) cc_final: 0.8596 (tpp80)
REVERT: B  217 MET cc_start: 0.7794 (ptt) cc_final: 0.7427 (ppp)
REVERT: B  239 ASN cc_start: 0.7384 (m-40) cc_final: 0.7090 (t0)
REVERT: B  246 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7879 (t0)
REVERT: B  254 ASP cc_start: 0.7777 (t0) cc_final: 0.6996 (p0)
REVERT: B  290 ASP cc_start: 0.6860 (m-30) cc_final: 0.6530 (m-30)
REVERT: B  298 ASP cc_start: 0.7943 (t70) cc_final: 0.7395 (t70)
REVERT: B  339 TRP cc_start: 0.8682 (m100) cc_final: 0.8076 (m-10)
REVERT: G   21 MET cc_start: 0.6892 (mtt) cc_final: 0.6449 (tmm)
REVERT: N   38 ARG cc_start: 0.7613 (ptt180) cc_final: 0.7136 (ptt-90)
REVERT: N  123 GLN cc_start: 0.7098 (tm-30) cc_final: 0.6848 (tm-30)
  outliers start: 28
  outliers final: 9
  residues processed: 119
  average time/residue: 0.6250
  time to fit residues: 78.8745
Evaluate side-chains
  107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  132 GLU
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   chunk 98 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 97 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.174561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.127996 restraints weight = 9804.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 3.18
r_work: 0.3604 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6299
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   8716  Z= 0.153
  Angle     :  0.552   8.254  11804  Z= 0.284
  Chirality :  0.042   0.148   1334
  Planarity :  0.004   0.047   1453
  Dihedral  :  6.506  57.882   1625
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.38 %
    Favored  : 81.94 %
  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:  1.04 (0.27), residues: 1024
  helix:  2.53 (0.25), residues: 429
  sheet: -0.13 (0.32), residues: 237
  loop : -1.05 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  27 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.011   0.001   TRP R  80 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8712)
  covalent geometry    : angle       0.55157 (11796)
  SS BOND              : bond        0.00135 (    4)
  SS BOND              : angle       0.81712 (    8)
  hydrogen bonds       : bond        0.04708 (  452)
  hydrogen bonds       : angle       4.45780 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  132 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7602 (mt-10)
REVERT: R  136 THR cc_start: 0.5598 (OUTLIER) cc_final: 0.5325 (p)
REVERT: A   34 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6583 (ttpt)
REVERT: A   60 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6453 (mpt)
REVERT: A  229 ASP cc_start: 0.7972 (t0) cc_final: 0.7435 (t0)
REVERT: A  314 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7296 (pm20)
REVERT: A  317 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8017 (ptt-90)
REVERT: A  392 GLU cc_start: 0.8022 (tt0) cc_final: 0.7240 (tp30)
REVERT: B   45 MET cc_start: 0.8212 (mmt) cc_final: 0.7458 (mtt)
REVERT: B   75 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7982 (mm110)
REVERT: B  134 ARG cc_start: 0.6484 (mtm-85) cc_final: 0.5501 (pmt170)
REVERT: B  138 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8348 (tp30)
REVERT: B  161 SER cc_start: 0.9112 (t) cc_final: 0.8682 (p)
REVERT: B  175 GLN cc_start: 0.7652 (mt0) cc_final: 0.7146 (mp10)
REVERT: B  180 PHE cc_start: 0.4955 (OUTLIER) cc_final: 0.2894 (p90)
REVERT: B  189 SER cc_start: 0.8401 (p) cc_final: 0.8161 (m)
REVERT: B  205 ASP cc_start: 0.7096 (p0) cc_final: 0.6793 (p0)
REVERT: B  214 ARG cc_start: 0.8884 (tpp80) cc_final: 0.8602 (tpp80)
REVERT: B  217 MET cc_start: 0.7791 (ptt) cc_final: 0.7441 (ppp)
REVERT: B  239 ASN cc_start: 0.7395 (m-40) cc_final: 0.7107 (t0)
REVERT: B  246 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7885 (t0)
REVERT: B  254 ASP cc_start: 0.7857 (t0) cc_final: 0.7044 (p0)
REVERT: B  290 ASP cc_start: 0.6765 (m-30) cc_final: 0.6391 (m-30)
REVERT: B  298 ASP cc_start: 0.7946 (t70) cc_final: 0.7398 (t70)
REVERT: B  339 TRP cc_start: 0.8655 (m100) cc_final: 0.8006 (m-10)
REVERT: G   21 MET cc_start: 0.6863 (mtt) cc_final: 0.6438 (tmm)
REVERT: N   38 ARG cc_start: 0.7582 (ptt180) cc_final: 0.7041 (ptm-80)
REVERT: N  105 ARG cc_start: 0.7498 (mtm180) cc_final: 0.6549 (mtm180)
  outliers start: 24
  outliers final: 12
  residues processed: 111
  average time/residue: 0.5939
  time to fit residues: 70.2447
Evaluate side-chains
  113 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  132 GLU
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.174011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.127276 restraints weight = 9679.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 3.21
r_work: 0.3582 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6441
moved from start:          0.4163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   8716  Z= 0.156
  Angle     :  0.553   9.037  11804  Z= 0.285
  Chirality :  0.042   0.148   1334
  Planarity :  0.004   0.048   1453
  Dihedral  :  6.502  57.815   1625
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.83 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.26), residues: 1024
  helix:  2.56 (0.25), residues: 429
  sheet: -0.10 (0.33), residues: 227
  loop : -1.09 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  27 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.012   0.001   TRP R 163 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8712)
  covalent geometry    : angle       0.55311 (11796)
  SS BOND              : bond        0.00132 (    4)
  SS BOND              : angle       0.82983 (    8)
  hydrogen bonds       : bond        0.04712 (  452)
  hydrogen bonds       : angle       4.43891 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: R  132 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7666 (mt-10)
REVERT: R  136 THR cc_start: 0.5764 (OUTLIER) cc_final: 0.5482 (p)
REVERT: A   60 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6566 (mpt)
REVERT: A  229 ASP cc_start: 0.7965 (t0) cc_final: 0.7451 (t0)
REVERT: A  314 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7437 (pm20)
REVERT: A  317 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.8042 (ptt-90)
REVERT: A  392 GLU cc_start: 0.8080 (tt0) cc_final: 0.7286 (tp30)
REVERT: B   45 MET cc_start: 0.8288 (mmt) cc_final: 0.7502 (mtt)
REVERT: B   46 ARG cc_start: 0.6921 (ttm-80) cc_final: 0.6423 (mtp-110)
REVERT: B  134 ARG cc_start: 0.6641 (mtm-85) cc_final: 0.5628 (pmt170)
REVERT: B  161 SER cc_start: 0.9138 (t) cc_final: 0.8746 (p)
REVERT: B  175 GLN cc_start: 0.7756 (mt0) cc_final: 0.7234 (mp10)
REVERT: B  180 PHE cc_start: 0.5218 (OUTLIER) cc_final: 0.3449 (p90)
REVERT: B  189 SER cc_start: 0.8433 (p) cc_final: 0.8200 (m)
REVERT: B  205 ASP cc_start: 0.7181 (p0) cc_final: 0.6849 (p0)
REVERT: B  214 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8621 (tpp80)
REVERT: B  217 MET cc_start: 0.7913 (ptt) cc_final: 0.7554 (ppp)
REVERT: B  239 ASN cc_start: 0.7490 (m-40) cc_final: 0.7197 (t0)
REVERT: B  246 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7851 (t0)
REVERT: B  254 ASP cc_start: 0.7913 (t0) cc_final: 0.7160 (p0)
REVERT: B  290 ASP cc_start: 0.6792 (m-30) cc_final: 0.6373 (m-30)
REVERT: B  298 ASP cc_start: 0.8054 (t70) cc_final: 0.7522 (t70)
REVERT: B  339 TRP cc_start: 0.8707 (m100) cc_final: 0.8020 (m-10)
REVERT: G   21 MET cc_start: 0.6966 (mtt) cc_final: 0.6548 (tmm)
REVERT: N   38 ARG cc_start: 0.7791 (ptt180) cc_final: 0.7235 (ptm-80)
REVERT: N  105 ARG cc_start: 0.7555 (mtm180) cc_final: 0.6729 (mtm180)
  outliers start: 25
  outliers final: 13
  residues processed: 109
  average time/residue: 0.6280
  time to fit residues: 72.6612
Evaluate side-chains
  107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   86 ILE
Chi-restraints excluded: chain R residue  132 GLU
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 52 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 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 = 0.176527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.129933 restraints weight = 9644.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 3.20
r_work: 0.3640 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6252
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086   8716  Z= 0.119
  Angle     :  0.525   9.879  11804  Z= 0.272
  Chirality :  0.041   0.147   1334
  Planarity :  0.004   0.049   1453
  Dihedral  :  6.126  58.267   1625
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.94 %
    Favored  : 81.83 %
  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:  1.24 (0.27), residues: 1024
  helix:  2.78 (0.25), residues: 428
  sheet: -0.10 (0.33), residues: 224
  loop : -0.96 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  27 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.016   0.001   TRP R 163 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8712)
  covalent geometry    : angle       0.52503 (11796)
  SS BOND              : bond        0.00073 (    4)
  SS BOND              : angle       0.63290 (    8)
  hydrogen bonds       : bond        0.04283 (  452)
  hydrogen bonds       : angle       4.30629 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: R  136 THR cc_start: 0.5279 (OUTLIER) cc_final: 0.4921 (p)
REVERT: A   60 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6386 (mpt)
REVERT: A  229 ASP cc_start: 0.7898 (t0) cc_final: 0.7349 (t0)
REVERT: A  314 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7405 (pm20)
REVERT: A  317 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8016 (ptt-90)
REVERT: A  392 GLU cc_start: 0.7910 (tt0) cc_final: 0.7139 (tp30)
REVERT: B   46 ARG cc_start: 0.6831 (ttm-80) cc_final: 0.6243 (mtp-110)
REVERT: B  134 ARG cc_start: 0.6532 (mtm-85) cc_final: 0.5534 (pmt170)
REVERT: B  175 GLN cc_start: 0.7647 (mt0) cc_final: 0.7141 (mp10)
REVERT: B  180 PHE cc_start: 0.4976 (OUTLIER) cc_final: 0.2995 (p90)
REVERT: B  189 SER cc_start: 0.8475 (p) cc_final: 0.8124 (m)
REVERT: B  205 ASP cc_start: 0.7012 (p0) cc_final: 0.6709 (p0)
REVERT: B  214 ARG cc_start: 0.8896 (tpp80) cc_final: 0.8599 (tpp80)
REVERT: B  217 MET cc_start: 0.7760 (ptt) cc_final: 0.7410 (ppp)
REVERT: B  239 ASN cc_start: 0.7389 (m-40) cc_final: 0.7162 (t0)
REVERT: B  246 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7787 (t0)
REVERT: B  254 ASP cc_start: 0.7828 (t0) cc_final: 0.7082 (p0)
REVERT: B  290 ASP cc_start: 0.6529 (m-30) cc_final: 0.6297 (m-30)
REVERT: B  298 ASP cc_start: 0.7908 (t70) cc_final: 0.7335 (t70)
REVERT: B  339 TRP cc_start: 0.8631 (m100) cc_final: 0.7956 (m-10)
REVERT: G   21 MET cc_start: 0.6849 (mtt) cc_final: 0.6478 (tmm)
REVERT: N   38 ARG cc_start: 0.7663 (ptt180) cc_final: 0.7180 (ptm-80)
REVERT: N  105 ARG cc_start: 0.7527 (mtm180) cc_final: 0.7288 (mtm180)
  outliers start: 20
  outliers final: 13
  residues processed: 109
  average time/residue: 0.5894
  time to fit residues: 68.3985
Evaluate side-chains
  108 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue   86 ILE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0870
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.176034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.131072 restraints weight = 9504.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 3.07
r_work: 0.3651 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6229
moved from start:          0.4313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   8716  Z= 0.121
  Angle     :  0.530   9.481  11804  Z= 0.273
  Chirality :  0.041   0.149   1334
  Planarity :  0.004   0.050   1453
  Dihedral  :  5.955  58.273   1625
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.94 %
    Favored  : 82.05 %
  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:  1.28 (0.27), residues: 1024
  helix:  2.79 (0.25), residues: 428
  sheet: -0.11 (0.33), residues: 224
  loop : -0.88 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  27 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.017   0.001   TRP R 163 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8712)
  covalent geometry    : angle       0.52952 (11796)
  SS BOND              : bond        0.00088 (    4)
  SS BOND              : angle       0.62539 (    8)
  hydrogen bonds       : bond        0.04281 (  452)
  hydrogen bonds       : angle       4.28164 ( 1308)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: R  136 THR cc_start: 0.5353 (OUTLIER) cc_final: 0.4991 (p)
REVERT: A   60 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6350 (mpt)
REVERT: A  229 ASP cc_start: 0.7874 (t0) cc_final: 0.7296 (t0)
REVERT: A  314 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7455 (pm20)
REVERT: A  317 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8018 (ptt-90)
REVERT: A  392 GLU cc_start: 0.7940 (tt0) cc_final: 0.7154 (tp30)
REVERT: B   46 ARG cc_start: 0.6730 (ttm-80) cc_final: 0.6117 (mtp-110)
REVERT: B   75 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7967 (mm110)
REVERT: B  134 ARG cc_start: 0.6633 (mtm-85) cc_final: 0.5614 (pmt170)
REVERT: B  175 GLN cc_start: 0.7614 (mt0) cc_final: 0.7121 (mp10)
REVERT: B  180 PHE cc_start: 0.4880 (OUTLIER) cc_final: 0.2954 (p90)
REVERT: B  189 SER cc_start: 0.8485 (p) cc_final: 0.8130 (m)
REVERT: B  205 ASP cc_start: 0.6970 (p0) cc_final: 0.6676 (p0)
REVERT: B  214 ARG cc_start: 0.8897 (tpp80) cc_final: 0.8606 (tpp80)
REVERT: B  217 MET cc_start: 0.7746 (ptt) cc_final: 0.7384 (ppp)
REVERT: B  239 ASN cc_start: 0.7378 (m-40) cc_final: 0.7166 (t0)
REVERT: B  246 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7785 (t0)
REVERT: B  254 ASP cc_start: 0.7823 (t0) cc_final: 0.7086 (p0)
REVERT: B  290 ASP cc_start: 0.6513 (m-30) cc_final: 0.6271 (m-30)
REVERT: B  298 ASP cc_start: 0.7899 (t70) cc_final: 0.7313 (t70)
REVERT: B  339 TRP cc_start: 0.8618 (m100) cc_final: 0.7950 (m-10)
REVERT: G   21 MET cc_start: 0.6923 (mtt) cc_final: 0.6603 (tmm)
REVERT: N   38 ARG cc_start: 0.7744 (ptt180) cc_final: 0.7259 (ptm-80)
REVERT: N  105 ARG cc_start: 0.7544 (mtm180) cc_final: 0.7318 (mtm180)
  outliers start: 18
  outliers final: 11
  residues processed: 103
  average time/residue: 0.6034
  time to fit residues: 66.0169
Evaluate side-chains
  107 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   83 VAL
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  180 PHE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  111 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0970
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
R 185 ASN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.176103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.131013 restraints weight = 9490.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 3.08
r_work: 0.3649 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6244
moved from start:          0.4313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120   8716  Z= 0.182
  Angle     :  0.951  59.180  11804  Z= 0.540
  Chirality :  0.046   0.784   1334
  Planarity :  0.004   0.050   1453
  Dihedral  :  5.957  58.274   1625
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.94 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.10 %
  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:  1.27 (0.27), residues: 1024
  helix:  2.79 (0.25), residues: 428
  sheet: -0.10 (0.33), residues: 224
  loop : -0.89 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  27 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.016   0.001   TRP R 163 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8712)
  covalent geometry    : angle       0.95078 (11796)
  SS BOND              : bond        0.00085 (    4)
  SS BOND              : angle       0.61985 (    8)
  hydrogen bonds       : bond        0.04291 (  452)
  hydrogen bonds       : angle       4.28105 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2856.65 seconds
wall clock time: 49 minutes 29.29 seconds (2969.29 seconds total)