Starting phenix.real_space_refine
on Thu Mar 13 01:23:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x8r_33057/03_2025/7x8r_33057_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x8r_33057/03_2025/7x8r_33057.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x8r_33057/03_2025/7x8r_33057.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x8r_33057/03_2025/7x8r_33057.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x8r_33057/03_2025/7x8r_33057_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x8r_33057/03_2025/7x8r_33057_neut.cif"
  }
  resolution = 2.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.143
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: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    5414      2.51       5
     N    1470      2.21       5
     O    1558      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8493
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1940
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2492
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 6, 'TRANS': 291}
          Chain breaks: 3
    Chain: "R"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 76
          Unusual residues: {'BYI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.60, per 1000 atoms: 0.66
  Number of scatterers: 8493
  At special positions: 0
  Unit cell: (79.254, 98.532, 155.295, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    1558      8.00
     N    1470      7.00
     C    5414      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    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
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " 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: 2.56
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1982

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      45.4% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.966A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 52 through 63
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.636A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.567A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.531A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (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 35
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 32 through 52
    Processing helix  chain 'R' and resid 138 through 170
      removed outlier: 4.522A  pdb=" N   ARG R 170 " --> pdb=" O   LEU R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 208
      removed outlier: 3.708A  pdb=" N   LYS R 202 " --> pdb=" O   ASP R 198 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 213 through 223
    Processing helix  chain 'R' and resid 223 through 256
      removed outlier: 3.921A  pdb=" N   ARG R 227 " --> pdb=" O   SER R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 275
      removed outlier: 3.516A  pdb=" N   LEU R 268 " --> pdb=" O   TRP R 264 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   GLY R 273 " --> pdb=" O   TYR R 269 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TRP R 274 " --> pdb=" O   VAL R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 292
      removed outlier: 3.679A  pdb=" N   VAL R 282 " --> pdb=" O   LEU R 278 " (cutoff:3.500A)
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 294 through 298
    Processing helix  chain 'R' and resid 302 through 338
      removed outlier: 3.930A  pdb=" N   TRP R 306 " --> pdb=" O   ASN R 302 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
    Processing helix  chain 'R' and resid 345 through 361
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 363 through 368
      removed outlier: 4.023A  pdb=" N   PHE R 367 " --> pdb=" O   HIS R 363 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 379 through 404
      removed outlier: 4.348A  pdb=" N   GLY R 395 " --> pdb=" O   THR R 391 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   LEU R 396 " --> pdb=" O   SER R 392 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 423
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.412A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.511A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.212A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.093A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.543A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.247A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.605A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.998A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.506A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.700A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (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 58 through 60
      removed outlier: 6.537A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    456 hydrogen bonds defined for protein.
    1290 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: 2.63

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1371
        1.31 -     1.43: 2474
        1.43 -     1.56: 4758
        1.56 -     1.68: 4
        1.68 -     1.81: 71
  Bond restraints: 8678
  Sorted by residual:
  bond pdb=" C42 BYI R 601 "
       pdb=" N41 BYI R 601 "
    ideal  model  delta    sigma   weight residual
    1.345  1.503 -0.158 2.00e-02 2.50e+03 6.22e+01
  bond pdb=" C15 BYI R 601 "
       pdb=" N17 BYI R 601 "
    ideal  model  delta    sigma   weight residual
    1.345  1.486 -0.141 2.00e-02 2.50e+03 4.98e+01
  bond pdb=" C51 BYI R 601 "
       pdb=" N50 BYI R 601 "
    ideal  model  delta    sigma   weight residual
    1.369  1.475 -0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" C06 BYI R 601 "
       pdb=" N08 BYI R 601 "
    ideal  model  delta    sigma   weight residual
    1.367  1.473 -0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" C51 BYI R 601 "
       pdb=" O53 BYI R 601 "
    ideal  model  delta    sigma   weight residual
    1.320  1.425 -0.105 2.00e-02 2.50e+03 2.74e+01
  ... (remaining 8673 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.49: 11722
        5.49 -    10.98: 31
       10.98 -    16.47: 1
       16.47 -    21.96: 1
       21.96 -    27.45: 1
  Bond angle restraints: 11756
  Sorted by residual:
  angle pdb=" N   ASN A 292 "
        pdb=" CA  ASN A 292 "
        pdb=" C   ASN A 292 "
      ideal   model   delta    sigma   weight residual
     111.40  123.55  -12.15 1.22e+00 6.72e-01 9.92e+01
  angle pdb=" C20 BYI R 601 "
        pdb=" C19 BYI R 601 "
        pdb=" C58 BYI R 601 "
      ideal   model   delta    sigma   weight residual
     119.62   92.17   27.45 3.00e+00 1.11e-01 8.37e+01
  angle pdb=" C18 BYI R 601 "
        pdb=" C19 BYI R 601 "
        pdb=" C58 BYI R 601 "
      ideal   model   delta    sigma   weight residual
     121.57  141.60  -20.03 3.00e+00 1.11e-01 4.46e+01
  angle pdb=" C   ILE R 147 "
        pdb=" N   TYR R 148 "
        pdb=" CA  TYR R 148 "
      ideal   model   delta    sigma   weight residual
     121.14  115.07    6.07 1.75e+00 3.27e-01 1.20e+01
  angle pdb=" N08 BYI R 601 "
        pdb=" C06 BYI R 601 "
        pdb=" O05 BYI R 601 "
      ideal   model   delta    sigma   weight residual
     108.72  118.47   -9.75 3.00e+00 1.11e-01 1.06e+01
  ... (remaining 11751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4638
       17.91 -    35.82: 425
       35.82 -    53.73: 88
       53.73 -    71.64: 20
       71.64 -    89.56: 13
  Dihedral angle restraints: 5184
    sinusoidal: 2120
      harmonic: 3064
  Sorted by residual:
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.27   19.73     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.81   18.19     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CB  CYS R 226 "
           pdb=" SG  CYS R 226 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -116.40   30.40     1      1.00e+01 1.00e-02 1.32e+01
  ... (remaining 5181 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1211
       0.087 -    0.174: 79
       0.174 -    0.262: 2
       0.262 -    0.349: 2
       0.349 -    0.436: 2
  Chirality restraints: 1296
  Sorted by residual:
  chirality pdb=" CA  ASN A 292 "
            pdb=" N   ASN A 292 "
            pdb=" C   ASN A 292 "
            pdb=" CB  ASN A 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.75e+00
  chirality pdb=" CG  LEU A 291 "
            pdb=" CB  LEU A 291 "
            pdb=" CD1 LEU A 291 "
            pdb=" CD2 LEU A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" C18 BYI R 601 "
            pdb=" C19 BYI R 601 "
            pdb=" C21 BYI R 601 "
            pdb=" C74 BYI R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -3.11   -2.77   -0.34 2.00e-01 2.50e+01 2.88e+00
  ... (remaining 1293 not shown)

  Planarity restraints: 1490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C19 BYI R 601 "   -0.016 2.00e-02 2.50e+03   1.34e-02 4.07e+00
        pdb=" C58 BYI R 601 "    0.035 2.00e-02 2.50e+03
        pdb=" C59 BYI R 601 "   -0.003 2.00e-02 2.50e+03
        pdb=" C60 BYI R 601 "    0.001 2.00e-02 2.50e+03
        pdb=" C61 BYI R 601 "    0.002 2.00e-02 2.50e+03
        pdb=" C62 BYI R 601 "   -0.001 2.00e-02 2.50e+03
        pdb=" C63 BYI R 601 "   -0.011 2.00e-02 2.50e+03
        pdb=" O64 BYI R 601 "   -0.003 2.00e-02 2.50e+03
        pdb=" O72 BYI R 601 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B  74 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.39e+00
        pdb=" C   SER B  74 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   SER B  74 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLN B  75 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO B 236 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1487 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 682
        2.74 -     3.28: 8482
        3.28 -     3.82: 14579
        3.82 -     4.36: 17817
        4.36 -     4.90: 30248
  Nonbonded interactions: 71808
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" ND1 HIS R 171 "
            pdb=" OE2 GLU R 412 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OD1 ASN A  23 "
            pdb=" N   LYS B  89 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.267 3.040
  ... (remaining 71803 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=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:             2.450
  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:             0.020
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.670
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:32.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
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      :  0.006   0.158   8678  Z= 0.352
  Angle     :  0.789  27.449  11756  Z= 0.372
  Chirality :  0.049   0.436   1296
  Planarity :  0.004   0.044   1490
  Dihedral  : 15.070  89.556   3193
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.26), residues: 1031
  helix:  1.61 (0.25), residues: 423
  sheet:  0.47 (0.33), residues: 231
  loop : -0.57 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.012   0.002   HIS A 357 
 PHE   0.017   0.002   PHE B 151 
 TYR   0.024   0.002   TYR B  59 
 ARG   0.006   0.000   ARG A  20 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 2.812 
Fit side-chains
REVERT: A  370 GLU cc_start: 0.7557 (pm20) cc_final: 0.7334 (pm20)
REVERT: R  418 GLU cc_start: 0.6225 (mm-30) cc_final: 0.5942 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 1.6562
  time to fit residues: 209.1470
Evaluate side-chains
  92 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0070
   chunk 30 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
R 394 GLN
R 410 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.197295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.148954 restraints weight = 8819.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.65
r_work: 0.3485 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8678  Z= 0.167
  Angle     :  0.527   6.710  11756  Z= 0.288
  Chirality :  0.041   0.158   1296
  Planarity :  0.004   0.043   1490
  Dihedral  :  7.411  56.570   1237
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.80 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1031
  helix:  2.16 (0.25), residues: 428
  sheet:  0.56 (0.33), residues: 228
  loop : -0.53 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  47 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.030   0.001   TYR R 148 
 ARG   0.004   0.000   ARG R 227 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 ASP cc_start: 0.8308 (t0) cc_final: 0.8081 (t0)
REVERT: A  299 GLU cc_start: 0.7685 (pt0) cc_final: 0.7346 (pt0)
REVERT: A  370 GLU cc_start: 0.8041 (pm20) cc_final: 0.7796 (pm20)
REVERT: B  217 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7959 (pp-130)
REVERT: B  270 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7538 (pp)
REVERT: R  170 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6467 (tpt170)
REVERT: R  418 GLU cc_start: 0.6441 (mm-30) cc_final: 0.6081 (mm-30)
  outliers start: 16
  outliers final: 3
  residues processed: 112
  average time/residue: 1.8299
  time to fit residues: 216.1311
Evaluate side-chains
  105 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  172 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 75 optimal weight:   20.0000
   chunk 78 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 91 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0980
   chunk 98 optimal weight:    0.0470
   chunk 49 optimal weight:    3.9990
   chunk 96 optimal weight:    0.7980
   overall best weight:    0.5680

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 177 ASN
R 240 ASN
R 410 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.198410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.150020 restraints weight = 8928.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.83
r_work: 0.3469 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8678  Z= 0.163
  Angle     :  0.497   7.000  11756  Z= 0.270
  Chirality :  0.041   0.170   1296
  Planarity :  0.003   0.043   1490
  Dihedral  :  6.845  53.214   1237
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.00 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1031
  helix:  2.40 (0.25), residues: 429
  sheet:  0.59 (0.32), residues: 228
  loop : -0.53 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.013   0.001   TYR R 402 
 ARG   0.009   0.000   ARG B 134 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A  299 GLU cc_start: 0.7775 (pt0) cc_final: 0.7434 (pt0)
REVERT: A  314 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7447 (mp0)
REVERT: A  370 GLU cc_start: 0.8133 (pm20) cc_final: 0.7880 (pm20)
REVERT: A  392 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7754 (mt-10)
REVERT: B  134 ARG cc_start: 0.7496 (ptp-110) cc_final: 0.7129 (mtm110)
REVERT: B  217 MET cc_start: 0.8282 (pmm) cc_final: 0.8001 (pp-130)
REVERT: B  270 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7598 (pp)
REVERT: R  170 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6577 (tpt170)
REVERT: R  391 THR cc_start: 0.8858 (m) cc_final: 0.8580 (p)
REVERT: R  418 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6044 (mm-30)
  outliers start: 20
  outliers final: 6
  residues processed: 117
  average time/residue: 1.8715
  time to fit residues: 230.2065
Evaluate side-chains
  113 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  172 LEU
Chi-restraints excluded: chain R residue  307 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 76 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 96 optimal weight:    0.7980
   chunk 63 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 177 ASN
R 410 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.197407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.150229 restraints weight = 8819.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 1.82
r_work: 0.3474 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8678  Z= 0.176
  Angle     :  0.500   6.786  11756  Z= 0.272
  Chirality :  0.041   0.176   1296
  Planarity :  0.003   0.044   1490
  Dihedral  :  6.694  52.174   1237
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 12.56 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.26), residues: 1031
  helix:  2.52 (0.25), residues: 428
  sheet:  0.56 (0.33), residues: 228
  loop : -0.54 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.014   0.001   TYR R 402 
 ARG   0.004   0.000   ARG B 134 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A  299 GLU cc_start: 0.7825 (pt0) cc_final: 0.7489 (pt0)
REVERT: A  314 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7425 (mp0)
REVERT: A  370 GLU cc_start: 0.8198 (pm20) cc_final: 0.7880 (pm20)
REVERT: A  392 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7827 (mt-10)
REVERT: B  134 ARG cc_start: 0.7614 (ptp-110) cc_final: 0.7275 (mtm110)
REVERT: B  217 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8103 (pp-130)
REVERT: B  270 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7680 (pp)
REVERT: R  170 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6586 (tpt170)
REVERT: R  391 THR cc_start: 0.8981 (m) cc_final: 0.8664 (p)
REVERT: R  410 GLN cc_start: 0.8067 (mt0) cc_final: 0.7841 (mt0)
REVERT: R  418 GLU cc_start: 0.6495 (mm-30) cc_final: 0.6153 (mm-30)
  outliers start: 26
  outliers final: 9
  residues processed: 114
  average time/residue: 1.5969
  time to fit residues: 191.2669
Evaluate side-chains
  115 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  314 GLU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  172 LEU
Chi-restraints excluded: chain R residue  307 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 70 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 73 optimal weight:   10.0000
   chunk 49 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 240 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.196834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149388 restraints weight = 8792.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.73
r_work: 0.3437 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8678  Z= 0.192
  Angle     :  0.507   6.773  11756  Z= 0.276
  Chirality :  0.042   0.183   1296
  Planarity :  0.003   0.044   1490
  Dihedral  :  6.635  51.626   1237
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.32 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.26), residues: 1031
  helix:  2.56 (0.25), residues: 428
  sheet:  0.57 (0.33), residues: 228
  loop : -0.52 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.016   0.001   PHE B 151 
 TYR   0.015   0.001   TYR R 402 
 ARG   0.003   0.000   ARG A 347 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A  299 GLU cc_start: 0.7895 (pt0) cc_final: 0.7542 (pt0)
REVERT: A  307 LYS cc_start: 0.7923 (mmmm) cc_final: 0.7666 (mmmt)
REVERT: A  370 GLU cc_start: 0.8199 (pm20) cc_final: 0.7910 (pm20)
REVERT: A  392 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7822 (mt-10)
REVERT: B  134 ARG cc_start: 0.7724 (ptp-110) cc_final: 0.7399 (mtm110)
REVERT: B  217 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8077 (pp-130)
REVERT: B  270 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7146 (pp)
REVERT: N  103 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.6275 (p90)
REVERT: R  170 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6542 (tpt170)
REVERT: R  410 GLN cc_start: 0.8078 (mt0) cc_final: 0.7832 (mt0)
REVERT: R  418 GLU cc_start: 0.6491 (mm-30) cc_final: 0.6153 (mm-30)
  outliers start: 22
  outliers final: 10
  residues processed: 114
  average time/residue: 1.7655
  time to fit residues: 211.0564
Evaluate side-chains
  116 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  172 LEU
Chi-restraints excluded: chain R residue  307 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0050
   chunk 37 optimal weight:    2.9990
   chunk 56 optimal weight:   20.0000
   overall best weight:    1.5600

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.194258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.146282 restraints weight = 8701.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 1.81
r_work: 0.3425 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8678  Z= 0.299
  Angle     :  0.578   6.786  11756  Z= 0.314
  Chirality :  0.045   0.186   1296
  Planarity :  0.004   0.044   1490
  Dihedral  :  6.872  52.548   1237
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.87 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.26), residues: 1031
  helix:  2.41 (0.25), residues: 427
  sheet:  0.47 (0.33), residues: 229
  loop : -0.56 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.010   0.002   HIS A 357 
 PHE   0.020   0.002   PHE B 151 
 TYR   0.021   0.002   TYR R 402 
 ARG   0.004   0.000   ARG B 251 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
REVERT: A  370 GLU cc_start: 0.8236 (pm20) cc_final: 0.8022 (pm20)
REVERT: A  392 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7873 (mt-10)
REVERT: B  134 ARG cc_start: 0.7764 (ptp-110) cc_final: 0.7475 (mtm110)
REVERT: B  217 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8220 (pmm)
REVERT: B  270 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7369 (pp)
REVERT: N  103 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.6374 (p90)
REVERT: R  170 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6714 (tpt170)
REVERT: R  391 THR cc_start: 0.8862 (m) cc_final: 0.8603 (p)
REVERT: R  412 GLU cc_start: 0.7214 (tp30) cc_final: 0.6657 (tp30)
REVERT: R  418 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6194 (mm-30)
  outliers start: 22
  outliers final: 9
  residues processed: 117
  average time/residue: 1.6587
  time to fit residues: 204.3022
Evaluate side-chains
  116 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  172 LEU
Chi-restraints excluded: chain R residue  307 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 394 GLN
R 410 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.195342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.147388 restraints weight = 8807.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 1.75
r_work: 0.3395 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8678  Z= 0.233
  Angle     :  0.534   6.769  11756  Z= 0.291
  Chirality :  0.043   0.187   1296
  Planarity :  0.004   0.045   1490
  Dihedral  :  6.760  52.379   1237
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.54 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.26), residues: 1031
  helix:  2.41 (0.25), residues: 427
  sheet:  0.50 (0.33), residues: 229
  loop : -0.58 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP N  47 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.018   0.001   PHE B 151 
 TYR   0.017   0.002   TYR R 402 
 ARG   0.003   0.000   ARG A 347 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8393 (m)
REVERT: A  370 GLU cc_start: 0.8176 (pm20) cc_final: 0.7939 (pm20)
REVERT: A  392 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7807 (mt-10)
REVERT: B  134 ARG cc_start: 0.7664 (ptp-110) cc_final: 0.7382 (mtm110)
REVERT: B  217 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8136 (pmm)
REVERT: B  270 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7276 (pp)
REVERT: N  103 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.6334 (p90)
REVERT: R  170 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6869 (tpt170)
REVERT: R  364 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: R  391 THR cc_start: 0.8796 (m) cc_final: 0.8507 (p)
REVERT: R  412 GLU cc_start: 0.7046 (tp30) cc_final: 0.6461 (tp30)
REVERT: R  418 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6145 (mm-30)
  outliers start: 26
  outliers final: 9
  residues processed: 116
  average time/residue: 1.5068
  time to fit residues: 184.4813
Evaluate side-chains
  117 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  172 LEU
Chi-restraints excluded: chain R residue  307 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 66 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 92 optimal weight:    6.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 410 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.196847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.149798 restraints weight = 8901.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 1.88
r_work: 0.3422 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8678  Z= 0.169
  Angle     :  0.497   6.733  11756  Z= 0.271
  Chirality :  0.041   0.189   1296
  Planarity :  0.003   0.045   1490
  Dihedral  :  6.580  51.775   1237
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.64 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.26), residues: 1031
  helix:  2.53 (0.25), residues: 428
  sheet:  0.51 (0.33), residues: 229
  loop : -0.54 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP N  47 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.016   0.001   PHE B 151 
 TYR   0.014   0.001   TYR R 148 
 ARG   0.003   0.000   ARG A 347 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
REVERT: A  248 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8284 (m)
REVERT: A  370 GLU cc_start: 0.8246 (pm20) cc_final: 0.8021 (pm20)
REVERT: A  392 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7873 (mt-10)
REVERT: B  134 ARG cc_start: 0.7696 (ptp-110) cc_final: 0.7381 (mtm110)
REVERT: B  217 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8106 (pp-130)
REVERT: N  103 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.6349 (p90)
REVERT: R  170 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6505 (tpt170)
REVERT: R  364 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7429 (mm-30)
REVERT: R  391 THR cc_start: 0.8906 (m) cc_final: 0.8610 (p)
REVERT: R  412 GLU cc_start: 0.7125 (tp30) cc_final: 0.6695 (tp30)
REVERT: R  418 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6163 (mm-30)
  outliers start: 19
  outliers final: 9
  residues processed: 119
  average time/residue: 1.6289
  time to fit residues: 204.6696
Evaluate side-chains
  119 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain R residue  170 ARG
Chi-restraints excluded: chain R residue  172 LEU
Chi-restraints excluded: chain R residue  307 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0030
   chunk 85 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 240 ASN
R 410 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.198089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.151151 restraints weight = 8838.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 1.83
r_work: 0.3466 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8678  Z= 0.144
  Angle     :  0.480   6.716  11756  Z= 0.262
  Chirality :  0.041   0.190   1296
  Planarity :  0.003   0.045   1490
  Dihedral  :  6.416  51.223   1237
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.41 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.26), residues: 1031
  helix:  2.67 (0.25), residues: 427
  sheet:  0.48 (0.33), residues: 230
  loop : -0.53 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 180 
 PHE   0.015   0.001   PHE R 169 
 TYR   0.014   0.001   TYR R 148 
 ARG   0.003   0.000   ARG A 347 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A  370 GLU cc_start: 0.8189 (pm20) cc_final: 0.7906 (pm20)
REVERT: B  134 ARG cc_start: 0.7534 (ptp-110) cc_final: 0.7213 (mtm110)
REVERT: B  217 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7964 (pp-130)
REVERT: B  270 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7661 (pp)
REVERT: R  364 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7362 (mm-30)
REVERT: R  391 THR cc_start: 0.8886 (m) cc_final: 0.8579 (p)
REVERT: R  412 GLU cc_start: 0.6874 (tp30) cc_final: 0.6520 (tp30)
REVERT: R  418 GLU cc_start: 0.6441 (mm-30) cc_final: 0.6112 (mm-30)
  outliers start: 15
  outliers final: 9
  residues processed: 116
  average time/residue: 1.5971
  time to fit residues: 194.7046
Evaluate side-chains
  116 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  172 LEU
Chi-restraints excluded: chain R residue  307 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0010
   chunk 39 optimal weight:    0.5980
   chunk 92 optimal weight:    4.9990
   chunk 99 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 21 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.197779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.149353 restraints weight = 8785.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 1.71
r_work: 0.3476 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8678  Z= 0.160
  Angle     :  0.489   6.714  11756  Z= 0.267
  Chirality :  0.041   0.191   1296
  Planarity :  0.003   0.045   1490
  Dihedral  :  6.417  51.253   1237
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.74 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.26), residues: 1031
  helix:  2.69 (0.25), residues: 427
  sheet:  0.46 (0.33), residues: 230
  loop : -0.53 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP N  47 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.014   0.001   TYR R 148 
 ARG   0.003   0.000   ARG A 347 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
REVERT: A  370 GLU cc_start: 0.8235 (pm20) cc_final: 0.7965 (pm20)
REVERT: A  392 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7644 (mt-10)
REVERT: B  134 ARG cc_start: 0.7667 (ptp-110) cc_final: 0.7358 (mtm110)
REVERT: B  217 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8095 (pp-130)
REVERT: B  270 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7696 (pp)
REVERT: R  364 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7383 (mm-30)
REVERT: R  412 GLU cc_start: 0.6768 (tp30) cc_final: 0.6386 (tp30)
REVERT: R  418 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6124 (mm-30)
  outliers start: 15
  outliers final: 10
  residues processed: 111
  average time/residue: 1.6181
  time to fit residues: 188.7562
Evaluate side-chains
  117 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  172 LEU
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  388 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 98 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0870
   chunk 17 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.8560

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 240 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.196506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.147988 restraints weight = 8898.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 1.73
r_work: 0.3448 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8678  Z= 0.198
  Angle     :  0.512   6.735  11756  Z= 0.279
  Chirality :  0.042   0.193   1296
  Planarity :  0.003   0.045   1490
  Dihedral  :  6.500  51.766   1237
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.07 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.26), residues: 1031
  helix:  2.64 (0.25), residues: 427
  sheet:  0.44 (0.33), residues: 231
  loop : -0.51 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.017   0.001   PHE B 151 
 TYR   0.016   0.001   TYR R 402 
 ARG   0.003   0.000   ARG A 347 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8237.20 seconds
wall clock time: 144 minutes 19.05 seconds (8659.05 seconds total)